Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'rms'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'xml2'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'roxygen2'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
alpha.proxy: no visible global function definition for 'filled.contour'
alpha.proxy: no visible global function definition for 'axis'
alpha.proxy: no visible global function definition for 'contour'
factor.model.stat: no visible global function definition for 'quantile'
factor.model.stat: no visible global function definition for 'lsfit'
partial.rainbow: no visible binding for global variable 'rainbow'
var.shrink.eqcor: no visible global function definition for 'var'
var.shrink.eqcor: no visible global function definition for 'quantile'
var.shrink.eqcor: no visible global function definition for 'cov2cor'
Undefined global functions or variables:
  axis contour cov2cor filled.contour lsfit quantile rainbow var
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "contour", "filled.contour")
  importFrom("stats", "cov2cor", "lsfit", "quantile", "var")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package unavailable to check Rd xrefs: 'Hmisc'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
plot.bursts: no visible global function definition for 'axis'
plot.bursts: no visible global function definition for 'arrows'
Undefined global functions or variables:
  arrows axis
Consider adding
  importFrom("graphics", "arrows", "axis")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'kknn'
Running examples in 'butcher-Ex.R' failed
The error most likely occurred in:

> ### Name: axe-kknn
> ### Title: Axing an kknn.
> ### Aliases: axe-kknn axe_call.kknn axe_env.kknn axe_fitted.kknn
> 
> ### ** Examples
> 
> # Load libraries
> suppressWarnings(suppressMessages(library(parsnip)))
> suppressWarnings(suppressMessages(library(rsample)))
> suppressWarnings(suppressMessages(library(rpart)))
> suppressWarnings(suppressMessages(library(kknn)))
Error in library(kknn) : there is no package called 'kknn'
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'riskRegression'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/BuyseTest/BuyseTest.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/bvarsv/bvarsv.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/bvartools/bvartools.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/bvls/bvls.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/bvpSolve/bvpSolve.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/BVSNLP/BVSNLP.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/bwd/bwd.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/bWGR/bWGR.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'jpeg', 'png'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/BWStest/BWStest.Rcheck/00install.out' for details.
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/bytescircle/bytescircle.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/bzinb/bzinb.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/c212/c212.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'igraph', 'qgraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/C50/C50.Rcheck/00install.out' for details.
Package required but not available: 'multichull'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cachem/cachem.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'XML'

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
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'markdown'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'Hmisc', 'RcmdrMisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cairoDevice/cairoDevice.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'png'

Package which this enhances but not available for checking: 'FastRWeb'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/Cairo/Cairo.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'pkgdown'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'taxize', 'pkgdown'

Packages suggested but not available for checking:
  'AnnotationDbi', 'KEGGREST', 'GO.db'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/calculus/calculus.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/calcWOI/calcWOI.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'ReGenesees'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'lintr'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'reticulate'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'spelling'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/CAMAN/CAMAN.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/CamelUp/CamelUp.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'spelling'
Running 'spelling.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(campfin)
  > 
  > test_check("campfin")
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (5)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-encoding.R:11:3): encoding for one file returns one row ───────
  nrow(enc) not equal to 1.
  1/1 mismatches
  [1] 0 - 1 == -1
  ── Failure (test-encoding.R:23:3): encoding for multiple files returns multiple rows ──
  nrow(enc) not equal to 50.
  1/1 mismatches
  [1] 0 - 50 == -50
  ── Failure (test-encoding.R:30:3): encoding for no file errors ─────────────────
  `file_encoding(tmp)` did not throw an error.
  
  [ FAIL 3 | WARN 0 | SKIP 5 | PASS 163 ]
  Error: Test failures
  Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'xml2'

Package suggested but not available for checking: 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'secr'

Packages suggested but not available for checking:
  'rgdal', 'ritis', 'taxize'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'leaflet', 'rgdal', 'sf', 'lwgeom'
Package unavailable to check Rd xrefs: 'sf'
Note: found 23 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

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

Package suggested but not available for checking: 'spelling'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'rgl'
Package unavailable to check Rd xrefs: 'rgl'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'Hmisc'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'png'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'sf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespaces in Imports field not imported from:
  'htmltools' 'shinydashboard'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
bootstrapCapwire: no visible global function definition for 'quantile'
drawCapRatesBeta : <anonymous>: no visible global function definition
  for 'rbeta'
drawCapRatesExp : <anonymous>: no visible global function definition
  for 'rexp'
drawCapRatesGamma : <anonymous>: no visible global function definition
  for 'rgamma'
drawCapRatesGeom : <anonymous>: no visible global function definition
  for 'rgeom'
drawCapRatesUnif : <anonymous>: no visible global function definition
  for 'runif'
partitionCountData : find.3.way.partitions: no visible global function
  definition for 'dmultinom'
Undefined global functions or variables:
  dmultinom quantile rbeta rexp rgamma rgeom runif
Consider adding
  importFrom("stats", "dmultinom", "quantile", "rbeta", "rexp", "rgamma",
             "rgeom", "runif")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'reticulate'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/carat/carat.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'leaflet', 'rgdal', 'spdep'

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

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

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.
Package suggested but not available for checking: 'rgl'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'sf', 'Hmisc'

Package suggested but not available for checking: 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Title field: should not end in a period.
Sub.pair: no visible global function definition for 'qnorm'
as.record: no visible global function definition for 'capture.output'
estN: no visible global function definition for 'sd'
estN: no visible global function definition for 'qnorm'
estN.bootstrap: no visible global function definition for 'runif'
Undefined global functions or variables:
  capture.output qnorm runif sd
Consider adding
  importFrom("stats", "qnorm", "runif", "sd")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'spelling'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'lintr'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/caret/caret.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'roxygen2'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
abundance: no visible global function definition for 'D'
Undefined global functions or variables:
  D
Consider adding
  importFrom("stats", "D")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'igraph', 'ggraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
barplotEQR: no visible global function definition for 'barplot'
barplotEQR: no visible global function definition for 'abline'
barplotEQR: no visible global function definition for 'par'
barplotEQR: no visible global function definition for 'text'
Undefined global functions or variables:
  abline barplot par text
Consider adding
  importFrom("graphics", "abline", "barplot", "par", "text")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'library' or 'require' calls in package code:
  'MASS' 'RSQLite' 'grid' 'sm'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'DESeq2', 'biomaRt'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'rgl'
Package unavailable to check Rd xrefs: 'rgl'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/carSurv/carSurv.Rcheck/00install.out' for details.
Packages required but not available: 'sf', 'igraph'

Package suggested but not available for checking: 'cartography'

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

Package suggested but not available for checking: 'rgdal'

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

Packages suggested but not available for checking:
  'lwgeom', 'SpatialPosition', 'rgdal'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'devtools', 'rlist', 'roxygen2', 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'igraph', 'tnet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespaces in Imports field not imported from:
  'janitor' 'tibble'
  All declared Imports should be used.
Note: found 75 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespaces in Imports field not imported from:
  'R6' 'crayon' 'dplyr' 'tidyr'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/CASMAP/CASMAP.Rcheck/00install.out' for details.
Package required but not available: 'bipartite'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/castor/castor.Rcheck/00install.out' for details.
Packages suggested but not available for checking:
  'mapview', 'sf', 'latticeExtra', 'stars'
Error(s) in re-building vignettes:
--- re-building 'AOA-tutorial.Rmd' using rmarkdown
Loading required package: raster
Loading required package: sp
Loading required package: lattice
Loading required package: ggplot2
Quitting from lines 33-42 (AOA-tutorial.Rmd) 
Error: processing vignette 'AOA-tutorial.Rmd' failed with diagnostics:
there is no package called 'sf'
--- failed re-building 'AOA-tutorial.Rmd'

--- re-building 'CAST-intro.Rmd' using rmarkdown
Quitting from lines 66-71 (CAST-intro.Rmd) 
Error: processing vignette 'CAST-intro.Rmd' failed with diagnostics:
there is no package called 'sf'
--- failed re-building 'CAST-intro.Rmd'

SUMMARY: processing the following files failed:
  'AOA-tutorial.Rmd' 'CAST-intro.Rmd'

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'igraph'
Error(s) in re-building vignettes:
--- re-building 'Introduction.Rmd' using rmarkdown
Installing package into 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cat2cat/cat2cat.Rcheck'
(as 'lib' is unspecified)
Warning: unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/4.2:
  cannot open URL 'http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/4.2/PACKAGES'
trying URL 'http://cran.rstudio.com/bin/windows/contrib/4.2/igraph_1.2.6.zip'
 length 5949867 bytes (5.7 MB)
==================================================
downloaded 5.7 MB

Quitting from lines 22-23 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
package 'igraph' not installed because it is not built for UCRT
--- failed re-building 'Introduction.Rmd'

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

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'sparklyr'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/catch/catch.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'spelling'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/catdap/catdap.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking:
  'rms', 'Ecdat', 'GAMBoost'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'Matrix'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'sva', 'leapp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
MDR.high.forward1: no visible global function definition for 'combn'
MDR.sing.mod1: no visible global function definition for 'combn'
MDR.sing.mod1: no visible global function definition for
  'complete.cases'
MDR.sing.mod1: no visible global function definition for 'lm'
MDR.sing.mod1: no visible global function definition for 'aov'
MDR.sing.mod1: no visible global function definition for 'anova'
MDR.stage.forward1: no visible global function definition for 'combn'
MDR.stage.forward1: no visible global function definition for
  'complete.cases'
MDR.stage.forward1: no visible global function definition for 'lm'
MDR.stage.forward1: no visible global function definition for 'resid'
MDR.stage.forward1: no visible global function definition for 'pf'
MDR_forward1: no visible global function definition for
  'complete.cases'
MDR_forward1: no visible global function definition for 'lm'
MDR_forward1: no visible global function definition for 'aov'
low.anova: no visible global function definition for 'complete.cases'
low.anova: no visible global function definition for 'lm'
sing.mod1: no visible global function definition for 'combn'
sing.mod1: no visible global function definition for 'complete.cases'
sing.mod1: no visible global function definition for 'lm'
sing.mod1: no visible global function definition for 'pf'
Undefined global functions or variables:
  anova aov combn complete.cases lm pf resid
Consider adding
  importFrom("stats", "anova", "aov", "complete.cases", "lm", "pf",
             "resid")
  importFrom("utils", "combn")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'Hmisc'

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

Package suggested but not available for checking: 'spacodiR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/catIrt/catIrt.Rcheck/00install.out' for details.
Packages required but not available: 'png', 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/catlearn/catlearn.Rcheck/00install.out' for details.
Package required but not available: 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/catnet/catnet.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/caTools/caTools.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cat/cat.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/CatReg/CatReg.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/catsim/catsim.Rcheck/00install.out' for details.
Malformed Description field: should contain one or more complete sentences.
ctab: no visible global function definition for 'xtabs'
mob.eqmain: no visible global function definition for 'model.matrix'
mob.qi: no visible global function definition for 'C'
mob.qi: no visible binding for global variable 'contr.treatment'
mob.rc1: no visible global function definition for 'C'
mob.rc1: no visible binding for global variable 'contr.treatment'
mob.rc1: no visible global function definition for 'model.matrix'
mob.symint: no visible global function definition for 'model.matrix'
print.ctab: no visible global function definition for 'ftable'
Undefined global functions or variables:
  C contr.treatment ftable model.matrix xtabs
Consider adding
  importFrom("stats", "C", "contr.treatment", "ftable", "model.matrix",
             "xtabs")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'RcppParallel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'lintr', 'roxygen2'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cattonum/cattonum.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'DiagrammeR', 'greta', 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'tidyverse', 'Hmisc', 'hrbrthemes', 'kableExtra'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Note: found 32 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'spelling'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'Hmisc'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

Package suggested but not available for checking: 'XML'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/CausalGPS/CausalGPS.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Note: found 1 marked UTF-8 string
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/CautiousLearning/CautiousLearning.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/caviarpd/caviarpd.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/CB2/CB2.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cba/cba.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'smotefamily'
Namespace in Imports field not imported from: 'prettydoc'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cbinom/cbinom.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cbird/cbird.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cblasr/cblasr.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'rstan', 'rstantools', 'StanHeaders'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'rgdal'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ccaPP/ccaPP.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'DiagrammeR'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
VD: no visible binding for global variable 'var'
stratcc : <anonymous>: no visible global function definition for
  'hclust'
stratcc : <anonymous>: no visible global function definition for
  'cutree'
Undefined global functions or variables:
  cutree hclust var
Consider adding
  importFrom("stats", "cutree", "hclust", "var")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cccp/cccp.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'igraph'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ccdrAlgorithm/ccdrAlgorithm.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'GeneNet'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cclust/cclust.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Malformed Description field: should contain one or more complete sentences.
p.Roy: no visible global function definition for 'pf'
p.asym: no visible global function definition for 'pf'
p.perm: no visible global function definition for 'cancor'
plt.asym: no visible global function definition for 'qf'
plt.asym: no visible global function definition for 'df'
plt.asym: no visible global function definition for 'abline'
plt.perm: no visible global function definition for 'hist'
plt.perm: no visible global function definition for 'mtext'
plt.perm: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline cancor df hist mtext pf qf
Consider adding
  importFrom("graphics", "abline", "hist", "mtext")
  importFrom("stats", "cancor", "df", "pf", "qf")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ccrtm/ccrtm.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cctools/cctools.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/CDatanet/CDatanet.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'library' or 'require' call to 'bitops' which was already attached by Depends.
  Please remove these calls from your code.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'sf', 'xml2', 'units'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cdcsis/cdcsis.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/CDLasso/CDLasso.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cdlTools/cdlTools.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/CDM/CDM.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'eemR'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'Seurat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cec2013/cec2013.Rcheck/00install.out' for details.
Note: found 907 marked UTF-8 strings
Running examples in 'CEDARS-Ex.R' failed
The error most likely occurred in:

> ### Name: create_project
> ### Title: Create a New CEDARS Project
> ### Aliases: create_project
> 
> ### ** Examples
> 
> # The code below creates an instance of CEDARS project on a public test MongoDB cluster, populated
> # with fictitious EHR corpora.
> 
> # MongoDB credentials
> db_user_name <- "testUser"
> db_user_pw <- "testPW"
> db_host <- "cedars.yvjp6.mongodb.net"
> db_port <- NA
> 
> # Using standard MongoDB URL format
> uri_fun <- mongo_uri_standard
> 
> # Name for MongoDB database which will contain the CEDARS project
> # In this case we generate a random name
> mongo_database <- find_project_name()
Error: No suitable servers found (`serverSelectionTryOnce` set): [TLS handshake failed: error:1416F086:SSL routines:tls_process_server_certificate:certificate verify failed calling ismaster on 'cedars-shard-00-00.yvjp6.mongodb.net:27017'] [TLS handshake failed: error:1416F086:SSL routines:tls_process_server_certificate:certificate verify failed calling ismaster on 'cedars-shard-00-01.yvjp6.mongodb.net:27017'] [TLS handshake failed: error:1416F086:SSL routines:tls_process_server_certificate:certificate ver
Execution halted
LaTeX errors when creating PDF version.
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Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ced/ced.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/CEGO/CEGO.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages in Depends field not imported from:
  'gplots' 'minpack.lm'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
erf: no visible global function definition for 'pnorm'
fitVolDist: no visible global function definition for 'nls.lm'
fitVolDist: no visible global function definition for 'nls.lm.control'
fitVolDist: no visible global function definition for 'optim'
fitVolDist: no visible global function definition for 'relist'
print.fitVolDist: no visible global function definition for 'coef'
print.fitVolDist: no visible global function definition for 'deviance'
print.fitVolDist: no visible global function definition for 'pt'
print.fitVolDist: no visible global function definition for
  'printCoefmat'
resFunChiSq: no visible global function definition for 'relist'
volEq7: no visible global function definition for 'integrate'
Undefined global functions or variables:
  coef deviance integrate nls.lm nls.lm.control optim pnorm
  printCoefmat pt relist
Consider adding
  importFrom("stats", "coef", "deviance", "integrate", "optim", "pnorm",
             "printCoefmat", "pt")
  importFrom("utils", "relist")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cellWise/cellWise.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/CENFA/CENFA.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cenROC/cenROC.Rcheck/00install.out' for details.
Packages required but not available: 'tidycensus', 'sf'

Package suggested but not available for checking: 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/censNID/censNID.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'chilemapas'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Unexported objects imported by ':::' calls:
  'copula:::dCdu' 'copula:::fitCopStart'
  See the note in ?`:::` about the use of this operator.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Malformed Description field: should contain one or more complete sentences.
MomNIT: no visible global function definition for 'dnorm'
MomNIT: no visible global function definition for 'pnorm'
cdfNI: no visible global function definition for 'pnorm'
cdfNI: no visible global function definition for 'pt'
em.cens: no visible global function definition for 'lm'
em.cens: no visible global function definition for 'coefficients'
em.cens : ft: no visible global function definition for 'dt'
em.cens : ft: no visible global function definition for 'pt'
em.cens: no visible global function definition for 'optimize'
em.cens: no visible global function definition for 'dnorm'
em.cens: no visible global function definition for 'pnorm'
em.cens: no visible global function definition for 'sd'
Undefined global functions or variables:
  coefficients dnorm dt lm optimize pnorm pt sd
Consider adding
  importFrom("stats", "coefficients", "dnorm", "dt", "lm", "optimize",
             "pnorm", "pt", "sd")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'png'
Namespace in Imports field not imported from: 'data.table'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'qdapTools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'xml2'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'sf'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

Package suggested but not available for checking: 'linkcomm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 104 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cepreader/cepreader.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
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Re-running with no redirection of stdout/stderr.
Packages required but not available: 'slippymath', 'spex', 'jpeg', 'png'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'alr3'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
select_lambda: no visible global function definition for 'median'
Undefined global functions or variables:
  median
Consider adding
  importFrom("stats", "median")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespaces in Imports field not imported from:
  'base' 'stats' 'tidyr'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'lmtest'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'knitr'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking:
  'Hmisc', 'randomForestSRC'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/CFC/CFC.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Malformed Description field: should contain one or more complete sentences.
cf_estimate_quantiles: no visible global function definition for
  'qnorm'
Undefined global functions or variables:
  qnorm
Consider adding
  importFrom("stats", "qnorm")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'rgdal'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'igraph'
Package unavailable to check Rd xrefs: 'causaleffect'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(cfid)
  > 
  > test_check("cfid")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-graphs.R:119:5): causaleffect / igraph supported ────────────────
  Error: there is no package called 'igraph'
  Backtrace:
      █
   1. └─base::loadNamespace(x) test-graphs.R:119:4
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base:::withOneRestart(expr, restarts[[1L]])
   4.       └─base:::doWithOneRestart(return(expr), restart)
  ── Error (test-graphs.R:125:5): generic igraph not supported ───────────────────
  Error: there is no package called 'igraph'
  Backtrace:
      █
   1. └─base::loadNamespace(x) test-graphs.R:125:4
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base:::withOneRestart(expr, restarts[[1L]])
   4.       └─base:::doWithOneRestart(return(expr), restart)
  ── Error (test-graphs.R:130:5): fail when no igraph ────────────────────────────
  Error: there is no package called 'igraph'
  Backtrace:
      █
   1. └─base::loadNamespace(x) test-graphs.R:130:4
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base:::withOneRestart(expr, restarts[[1L]])
   4.       └─base:::doWithOneRestart(return(expr), restart)
  ── Error (test-graphs.R:167:5): causaleffect sanity ────────────────────────────
  Error: Package `igraph` is not available for export
  Backtrace:
      █
   1. └─cfid::export_graph(g, "causaleffect") test-graphs.R:167:4
   2.   └─cfid:::stop_("Package `igraph` is not available for export")
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 109 ]
  Error: Test failures
  Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cgAUC/cgAUC.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/CGGP/CGGP.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cghRA/cghRA.Rcheck/00install.out' for details.
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cglm/cglm.Rcheck/00install.out' for details.
Package required but not available: 'XML'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/CGManalyzer/CGManalyzer.Rcheck/00install.out' for details.
Package required but not available: 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'hrbrthemes'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cgraph/cgraph.Rcheck/00install.out' for details.
Packages required but not available: 'Hmisc', 'rms'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package unavailable to check Rd xrefs: 'sf'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'umap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'vdiffr'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/changepoint.mv/changepoint.mv.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/changepoint.np/changepoint.np.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/changepoint/changepoint.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/changepointsHD/changepointsHD.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ChangePointTaylor/ChangePointTaylor.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/changepointTests/changepointTests.Rcheck/00install.out' for details.
Package required but not available: 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ChannelAttribution/ChannelAttribution.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/Chaos01/Chaos01.Rcheck/00install.out' for details.
Packages required but not available: 'rgl', 'sphereplot'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ChargeTransport/ChargeTransport.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'library' or 'require' call to 'RCurl' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'RCurl' 'bitops' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
createDataset: no visible global function definition for 'read.csv'
createInventory: no visible global function definition for 'read.csv'
downloadMaster: no visible global function definition for
  'getURLContent'
downloadMaster: no visible global function definition for 'read.csv'
downloadMaster: no visible global function definition for 'write.csv'
getMissingScrape: no visible global function definition for 'read.csv'
readLocalMaster: no visible global function definition for 'read.csv'
readMonthlyCsv: no visible global function definition for 'read.csv'
scrapeToCsv: no visible global function definition for 'download.file'
writeData: no visible global function definition for 'write.csv'
writeGhcn: no visible global function definition for 'write.table'
writeInventory: no visible global function definition for 'write.table'
writeMonthlyStations: no visible global function definition for
  'read.csv'
writeMonthlyStations: no visible global function definition for
  'write.csv'
Undefined global functions or variables:
  download.file getURLContent read.csv write.csv write.table
Consider adding
  importFrom("utils", "download.file", "read.csv", "write.csv",
             "write.table")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'textreadr'

Packages suggested but not available for checking:
  'devtools', 'tidygraph', 'ggraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'rappdirs' 'stringr'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/chebpol/chebpol.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cheb/cheb.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Malformed Description field: should contain one or more complete sentences.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'devtools'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/checkmate/checkmate.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'units'
'LazyData' is specified without a 'data' directory
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(checkr)
  > 
  > test_check("checkr")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-vector.R:37:3): vector with units ───────────────────────────────
  Error: there is no package called 'units'
  Backtrace:
      █
   1. └─base::loadNamespace(x) test-vector.R:37:2
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base:::withOneRestart(expr, restarts[[1L]])
   4.       └─base:::doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 352 ]
  Error: Test failures
  Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cheddar/cheddar.Rcheck/00install.out' for details.
Package required but not available: 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'rcdk', 'MSQC'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'mlrMBO', 'mlr'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking:
  'rgl', 'speaq', 'hyperSpec'
Package unavailable to check Rd xrefs: 'rgl'
Running examples in 'ChemoSpec-Ex.R' failed
The error most likely occurred in:

> ### Name: clupaSpectra
> ### Title: Hierarchical Cluster-Based Peak Alignment on a Spectra Object
> ### Aliases: clupaSpectra
> ### Keywords: utilities
> 
> ### ** Examples
> 
> 
> data(alignMUD)
> 
> plotSpectra(alignMUD,
+   which = 1:20, lab.pos = 4.5, offset = 0.1,
+   yrange = c(0, 1900), amp = 500, xlim = c(1.5, 1.8),
+   main = "Misaligned NMR Spectra (alignMUD)"
+ )
> 
> aMUD <- clupaSpectra(alignMUD)
Error in clupaSpectra(alignMUD) : 
  You need to install package speaq to use this function
Execution halted
LaTeX errors when creating PDF version.
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Package suggested but not available for checking: 'roxut'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'reticulate'

Package suggested but not available for checking: 'png'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'spelling'
Namespace in Imports field not imported from: 'generics'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking:
  'GenomicInteractions', 'Gviz', 'countreg'
Namespaces in Imports field not imported from:
  'knitr' 'rmarkdown'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'RcppParallel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'spelling'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'gamlss.dist'
  All declared Imports should be used.
Note: found 29 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'sf', 'rmapshaper'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'chillR'
Package unavailable to check Rd xrefs: 'chillR'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'XML'

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 required but not available: 'bruceR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'qpcR', 'RDML', 'spelling'
Package unavailable to check Rd xrefs: 'qpcR'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ChIPtest/ChIPtest.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'sf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/CHMM/CHMM.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'magrittr'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/chngpt/chngpt.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/CHNOSZ/CHNOSZ.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
File
  LICENSE
is not mentioned in the DESCRIPTION file.
choicemodelr : drawDelta: no visible global function definition for
  'rnorm'
choicemodelr : mnlRwMetropOnce: no visible global function definition
  for 'rnorm'
choicemodelr : mnlRwMetropOnce: no visible global function definition
  for 'runif'
choicemodelr : rmultireg: no visible global function definition for
  'rnorm'
choicemodelr : rwishart: no visible global function definition for
  'rchisq'
choicemodelr : rwishart: no visible global function definition for
  'rnorm'
choicemodelr : fsh: no visible global function definition for
  'flush.console'
choicemodelr: no visible global function definition for 'matplot'
choicemodelr: no visible global function definition for 'write.table'
Undefined global functions or variables:
  flush.console matplot rchisq rnorm runif write.table
Consider adding
  importFrom("graphics", "matplot")
  importFrom("stats", "rchisq", "rnorm", "runif")
  importFrom("utils", "flush.console", "write.table")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'igraph', 'threejs'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/CholWishart/CholWishart.Rcheck/00install.out' for details.
Malformed Description field: should contain one or more complete sentences.
Qh.times.dhyper: no visible global function definition for 'var'
Qh.times.dhyper: no visible global function definition for 'pnorm'
Qh.times.dhyper: no visible global function definition for 'dhyper'
TDiM: no visible global function definition for 'sd'
choplump.default: no visible global function definition for
  'flush.console'
choplump.formula: no visible global function definition for 'terms'
cm.compact: no visible global function definition for 'dhyper'
Undefined global functions or variables:
  dhyper flush.console pnorm sd terms var
Consider adding
  importFrom("stats", "dhyper", "pnorm", "sd", "terms", "var")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/chopthin/chopthin.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available:
  'acs', 'Hmisc', 'ggmap', 'RgoogleMaps', 'tigris', 'xml2', 'rvest',
  'tidycensus'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'xml2', 'rvest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'roxygen2'
Malformed Description field: should contain one or more complete sentences.
parse_counts: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'htmltools'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'base'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'devtools'
Namespaces in Imports field not imported from:
  'DT' 'dplyr' 'prettydoc' 'rmdformats' 'skimr'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'vdiffr'
Namespaces in Imports field not imported from:
  'dplyr' 'magick' 'tidyr'
  All declared Imports should be used.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tibble)
  > library(ggplot2)
  > library(vdiffr)
  Error in library(vdiffr) : there is no package called 'vdiffr'
  Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'jpeg', 'rgdal'
Running examples in 'chronosphere-Ex.R' failed
The error most likely occurred in:

> ### Name: mapedge
> ### Title: Function to quickly draft the edge of the equirectangular
> ###   projection
> ### Aliases: mapedge
> 
> ### ** Examples
> 
> # requires rgdal
> edge <- mapedge()
> molledge <- spTransform(edge, CRS("+proj=moll"))
Error in spTransform(edge, CRS("+proj=moll")) : 
  package rgdal is required for spTransform methods
Calls: spTransform -> spTransform
Execution halted
Error(s) in re-building vignettes:
--- re-building 'chronosphere.Rmd' using rmarkdown
pdftex: major issue: User/administrator updates are out-of-sync.
pdfcrop: major issue: User/administrator updates are out-of-sync.
pdftex: major issue: User/administrator updates are out-of-sync.
pdfcrop: major issue: User/administrator updates are out-of-sync.
pdftex: major issue: User/administrator updates are out-of-sync.
pdfcrop: major issue: User/administrator updates are out-of-sync.
pdftex: major issue: User/administrator updates are out-of-sync.
pdfcrop: major issue: User/administrator updates are out-of-sync.
Quitting from lines 354-365 (chronosphere.Rmd) 
Error: processing vignette 'chronosphere.Rmd' failed with diagnostics:
This method requires the 'rgdal' package to run.
--- failed re-building 'chronosphere.Rmd'

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

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/chron/chron.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/CHsharp/CHsharp.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'spelling'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/chunkR/chunkR.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespaces in Imports field not imported from:
  'Matrix' 'stringr'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'R6'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/CIFsmry/CIFsmry.Rcheck/00install.out' for details.
Packages required but not available: 'xml2', 'gifti'

Package suggested but not available for checking: 'rgl'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'twang', 'arm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available:
  'ChIPseeker', 'DESeq2', 'sva', 'TxDb.Hsapiens.UCSC.hg38.knownGene',
  'TxDb.Hsapiens.UCSC.hg19.knownGene',
  'TxDb.Mmusculus.UCSC.mm10.knownGene'

Package suggested but not available for checking: 'biomaRt'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available:
  'igraph', 'centiserve', 'qdapTools', 'intergraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
cin: no visible global function definition for 'pnorm'
gammaHRF: no visible global function definition for 'dgamma'
intertest: no visible global function definition for 'pnorm'
truncSum: no visible global function definition for 'spline'
Undefined global functions or variables:
  dgamma pnorm spline
Consider adding
  importFrom("stats", "dgamma", "pnorm", "spline")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cinterpolate/cinterpolate.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'userfriendlyscience'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/circglmbayes/circglmbayes.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'spelling'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'ComplexHeatmap', 'png'
Unavailable namespace imported from by a ':::' call: 'ComplexHeatmap'
  See the note in ?`:::` about the use of this operator.
Running examples in 'circlize-Ex.R' failed
The error most likely occurred in:

> ### Name: circos.raster
> ### Title: Add raster images
> ### Aliases: circos.raster
> 
> ### ** Examples
> 
> require(png)
Loading required package: png
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'png'
> image = system.file("extdata", "Rlogo.png", package = "circlize")
> image = as.raster(readPNG(image))
Error in readPNG(image) : could not find function "readPNG"
Calls: as.raster
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/CircSpaceTime/CircSpaceTime.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/CircularDDM/CircularDDM.Rcheck/00install.out' for details.
Package required but not available: 'NPCirc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/circular/circular.Rcheck/00install.out' for details.
Packages suggested but not available for checking:
  'kableExtra', 'roxygen2', 'vdiffr'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/circumplex/circumplex.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cIRT/cIRT.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'RGtk2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
cit.assignBcmst: no visible binding for global variable 'citbcmst'
cit.assignBcmst : <anonymous>: no visible global function definition
  for 'median'
cit.assignBcmst: no visible global function definition for 'prcomp'
cit.assignBcmst: no visible global function definition for 'par'
cit.assignBcmst: no visible global function definition for 'lines'
cit.assignBcmst: no visible global function definition for 'legend'
cit.centroids : <anonymous>: no visible global function definition for
  'median'
cit.centroids : <anonymous>: no visible global function definition for
  'var'
cit.dist: no visible global function definition for 'dist'
cit.dist: no visible global function definition for 'as.dist'
cit.dist: no visible global function definition for 'cor'
cit.distToCentroids: no visible global function definition for
  'quantile'
cit.distToCentroids : <anonymous>: no visible global function
  definition for 'median'
cit.distToCentroids : <anonymous>: no visible global function
  definition for 'mad'
Undefined global functions or variables:
  as.dist citbcmst cor dist legend lines mad median par prcomp quantile
  var
Consider adding
  importFrom("graphics", "legend", "lines", "par")
  importFrom("stats", "as.dist", "cor", "dist", "mad", "median",
             "prcomp", "quantile", "var")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
cit.assignCcmst: no visible binding for global variable 'citccmst'
cit.assignCcmst : <anonymous>: no visible global function definition
  for 'median'
cit.assignCcmst : median.na: no visible global function definition for
  'median'
cit.assignCcmst: no visible global function definition for 'prcomp'
cit.assignCcmst: no visible global function definition for 'par'
cit.assignCcmst: no visible global function definition for 'lines'
cit.assignCcmst: no visible global function definition for 'legend'
cit.centroids : <anonymous>: no visible global function definition for
  'median'
cit.centroids : <anonymous>: no visible global function definition for
  'var'
cit.dist: no visible global function definition for 'dist'
cit.dist: no visible global function definition for 'as.dist'
cit.dist: no visible global function definition for 'cor'
cit.distToCentroids: no visible global function definition for
  'quantile'
cit.distToCentroids : <anonymous>: no visible global function
  definition for 'median'
cit.distToCentroids : <anonymous>: no visible global function
  definition for 'mad'
Undefined global functions or variables:
  as.dist citccmst cor dist legend lines mad median par prcomp quantile
  var
Consider adding
  importFrom("graphics", "legend", "lines", "par")
  importFrom("stats", "as.dist", "cor", "dist", "mad", "median",
             "prcomp", "quantile", "var")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'arm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cit/cit.Rcheck/00install.out' for details.
Malformed Description field: should contain one or more complete sentences.
CityPlot: no visible global function definition for 'read.table'
CityPlot: no visible global function definition for 'tail'
CityPlot: no visible global function definition for 'pdf'
CityPlot: no visible global function definition for 'split.screen'
CityPlot: no visible global function definition for 'screen'
CityPlot: no visible global function definition for 'par'
CityPlot: no visible global function definition for 'rect'
CityPlot: no visible global function definition for 'text'
CityPlot: no visible global function definition for 'lines'
CityPlot: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  dev.off lines par pdf read.table rect screen split.screen tail text
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "lines", "par", "rect", "screen",
             "split.screen", "text")
  importFrom("utils", "read.table", "tail")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available:
  'dataRetrieval', 'EcoHydRology', 'geoknife'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'roxygen2'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/civis/civis.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'shinyBS'
  All declared Imports should be used.
Note: found 29 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'sf', 'xml2'
Packages unavailable to check Rd xrefs: 'xml2', 'sf'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/CKLRT/CKLRT.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/Ckmeans.1d.dp/Ckmeans.1d.dp.Rcheck/00install.out' for details.
Packages required but not available: 'ggraph', 'igraph', 'tidygraph'

Package suggested but not available for checking: 'tidyverse'

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

Package suggested but not available for checking: 'rgl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cladoRcpp/cladoRcpp.Rcheck/00install.out' for details.
Package required but not available: 'rgl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'png'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'rggobi'
'library' or 'require' call to 'rggobi' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
generate_data : <anonymous>: no visible global function definition for
  'runif'
knnf: no visible global function definition for 'terms'
rescaler.default: no visible global function definition for 'sd'
rescaler.default: no visible global function definition for 'median'
rescaler.default: no visible global function definition for 'mad'
simvar.numeric: no visible global function definition for 'runif'
Undefined global functions or variables:
  mad median runif sd terms
Consider adding
  importFrom("stats", "mad", "median", "runif", "sd", "terms")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'units'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/classInt/classInt.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'rpart'
  All declared Imports should be used.
Note: found 9 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/class/class.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'readtext'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cld2/cld2.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cld3/cld3.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cleancall/cleancall.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Warnings in file 'R/currency.R':
  unable to translate '<U+20AC>' to native encoding
  unable to translate '<U+00A5>' to native encoding
  unable to translate '<U+00A3>' to native encoding
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'reticulate'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Skipping vignette re-building
Packages suggested but not available for checking: 'devtools', 'rasciidoc'

VignetteBuilder package required for checking but not installed: 'rasciidoc'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available:
  'ggtext', 'transformr', 'imputeTestbench', 'imputeTS'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/clere/clere.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/clevr/clevr.Rcheck/00install.out' for details.
Package required but not available: 'sf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'xml2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ClickClust/ClickClust.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/clifford/clifford.Rcheck/00install.out' for details.
Packages required but not available: 'xml2', 'rvest'

Package suggested but not available for checking: 'spelling'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'jpeg', 'sf'
Running examples in 'climaemet-Ex.R' failed
The error most likely occurred in:

> ### Name: ggstripes
> ### Title: Warming stripes graph
> ### Aliases: ggstripes
> 
> ### ** Examples
> 
> 
> 
> library(ggplot2)
> 
> data <- climaemet::climaemet_9434_temp
> 
> ggstripes(data, plot_title = "Zaragoza Airport") +
+   labs(subtitle = "(1950-2020)")
Climate stripes plotting ...
> 
> ggstripes(data, plot_title = "Zaragoza Airport", plot_type = "trend") +
+   labs(subtitle = "(1950-2020)")
Climate stripes with temperature line trend plotting ...
Error in loadNamespace(x) : there is no package called 'jpeg'
Calls: ggstripes ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'XML'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'rangeBuilder'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'MODISTools', 'sf'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/climdex.pcic/climdex.pcic.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'scio'
clime: no visible global function definition for 'cov'
cv.clime: no visible global function definition for 'cov'
cv.clime: no visible binding for global variable 'sd'
Undefined global functions or variables:
  cov sd
Consider adding
  importFrom("stats", "cov", "sd")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'PlackettLuce'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking:
  'inTextSummaryTable', 'xml2'
Package unavailable to check Rd xrefs: 'inTextSummaryTable'
Running examples in 'clinDataReview-Ex.R' failed
The error most likely occurred in:

> ### Name: barplotClinData
> ### Title: Barplot interactive plot.
> ### Aliases: barplotClinData
> 
> ### ** Examples
> 
> library(clinUtils)
> 
> data(dataADaMCDISCP01)
> labelVars <- attr(dataADaMCDISCP01, "labelVars")
> 
> dataAE <- dataADaMCDISCP01$ADAE
> dataDM <- dataADaMCDISCP01$ADSL
> 
> ## example of basic barplot:
> 
> # treemap takes as input table with counts
> library(inTextSummaryTable)
Error in library(inTextSummaryTable) : 
  there is no package called 'inTextSummaryTable'
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'rstan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/clinfun/clinfun.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ClinicalTrialSummary/ClinicalTrialSummary.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'reticulate'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'xml2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
gxe.cc: no visible global function definition for 'qnorm'
gxe.coh: no visible global function definition for 'qnorm'
utility.cc: no visible global function definition for 'qnorm'
utility.coh: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  qnorm
Consider adding
  importFrom("stats", "qnorm")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'flextable'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(clinUtils)
  > 
  > test_check("clinUtils")
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (2)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_knitPrintListPlots.R:10:1): (code run outside of `test_that()`) ──
  Error: there is no package called 'flextable'
  Backtrace:
      █
   1. └─base::library(flextable) test_knitPrintListPlots.R:10:0
  
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 272 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'clinUtils-vignette.Rmd' using rmarkdown

Attaching package: 'htmltools'

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

    p

Import AE dataset.
Import CM dataset.
Import DM dataset.
Import EX dataset.
Import LB dataset.
Import MH dataset.
Import SV dataset.
Import VS dataset.
Warning: Ignoring unknown parameters: binwidth, bins, pad
Warning: Ignoring unknown parameters: binwidth, bins, pad
Warning: Ignoring unknown parameters: binwidth, bins, pad

Attaching package: 'plotly'

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

    arrange, mutate, rename, summarise

The following object is masked from 'package:ggplot2':

    last_plot

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

    filter

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

    layout

Quitting from lines 499-514 (clinUtils-vignette.Rmd) 
Error: processing vignette 'clinUtils-vignette.Rmd' failed with diagnostics:
there is no package called 'flextable'
--- failed re-building 'clinUtils-vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'igraph', 'qgraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cli/cli.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/clock/clock.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/clogitboost/clogitboost.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/clogitL1/clogitL1.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'tfruns'

Packages suggested but not available for checking: 'tensorflow', 'keras'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'kableExtra', 'lintr'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'XML'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/clpAPI/clpAPI.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
socp: no visible global function definition for 'as'
Undefined global functions or variables:
  as
Consider adding
  importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/clue/clue.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cluscov/cluscov.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ClusPred/ClusPred.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/clusrank/clusrank.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'utils'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

Package suggested but not available for checking: 'Seurat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Found the following significant warnings:
  Warning: 'memory.limit()' is no longer supported
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/clustDRM/clustDRM.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'DT'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'qrcm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/clusterCrit/clusterCrit.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/clustering.sc.dp/clustering.sc.dp.Rcheck/00install.out' for details.
Packages required but not available: 'GSEABase', 'GSVA', 'singscore'

Package suggested but not available for checking: 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'devtools', 'roxygen2'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/clustermq/clustermq.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'tidyverse'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/clusterPower/clusterPower.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cluster/cluster.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'OpenImageR'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ClusterR/ClusterR.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'rgl'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'spdep'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'Hmisc', 'spelling'
Error(s) in re-building vignettes:
--- re-building 'Example_on_simulated_data.Rmd' using rmarkdown
Quitting from lines 25-27 (Example_on_simulated_data.Rmd) 
Error: processing vignette 'Example_on_simulated_data.Rmd' failed with diagnostics:
there is no package called 'Hmisc'
--- failed re-building 'Example_on_simulated_data.Rmd'

--- re-building 'description_of_algorithm.Rnw' using Sweave
texify: C:\jenkins\workspace\miktex\windows\build\source\Libraries\MiKTeX\Core\Utils\Utils.cpp:490: internal error

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

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

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ClustMMDD/ClustMMDD.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

Package suggested but not available for checking: 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'ggraph', 'igraph', 'tidygraph'

Packages suggested but not available for checking:
  'Seurat', 'pkgdown', 'spelling'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'MASS' 'cluster' 'datasets' 'dplyr' 'klaR' 'psycho' 'shiny'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
braycurtis: no visible global function definition for 'as.dist'
czekanowski: no visible global function definition for 'as.dist'
findComplementaryIndices: no visible global function definition for
  'na.omit'
genSimilarityProfile: no visible global function definition for 'dist'
simprof: no visible global function definition for 'dist'
simprof: no visible global function definition for 'hclust'
simprof.plot : <local> : colorizer: no visible global function
  definition for 'is.leaf'
simprof.plot: no visible global function definition for 'rainbow'
simprof.plot: no visible global function definition for 'dendrapply'
simprof.plot: no visible global function definition for 'as.dendrogram'
Undefined global functions or variables:
  as.dendrogram as.dist dendrapply dist hclust is.leaf na.omit rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("stats", "as.dendrogram", "as.dist", "dendrapply", "dist",
             "hclust", "is.leaf", "na.omit")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ClustVarLV/ClustVarLV.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ClusVis/ClusVis.Rcheck/00install.out' for details.
Packages suggested but not available for checking:
  'annotate', 'GO.db', 'moe430a.db'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/clv/clv.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/CLVTools/CLVTools.Rcheck/00install.out' for details.
cma_es: no visible global function definition for 'rnorm'
f_rand: no visible global function definition for 'runif'
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'Rdpack'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'spelling'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'Ryacas0'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Malformed Description field: should contain one or more complete sentences.
alpha.cronbach: no visible global function definition for 'cov'
alpha.curve: no visible global function definition for 'text'
Undefined global functions or variables:
  cov text
Consider adding
  importFrom("graphics", "text")
  importFrom("stats", "cov")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cmenet/cmenet.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/CMF/CMF.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'kableExtra'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cmfrec/cmfrec.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'devtools', 'roxygen2'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'twang'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cmprskQR/cmprskQR.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cmprsk/cmprsk.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking:
  'cmsaf', 'cmsafvis', 'spelling'
Package unavailable to check Rd xrefs: 'cmsaf'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'cmsafvis'

Package suggested but not available for checking: 'spelling'

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

Packages suggested but not available for checking:
  'plotKML', 'rnaturalearth', 'spelling'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'Matrix' 'caret' 'e1071' 'epitools' 'shiny' 'shinyMatrix'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'rvest', 'xml2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'lintr', 'spelling', 'vdiffr'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespaces in Imports field not imported from:
  'htmltools' 'htmlwidgets' 'readxl' 'testthat' 'widgetframe'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cnaOpt/cnaOpt.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cna/cna.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'rgl', 'shapes'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
copynumberBootstrap: no visible global function definition for
  'txtProgressBar'
copynumberBootstrap: no visible global function definition for
  'quantile'
copynumberBootstrap: no visible global function definition for
  'setTxtProgressBar'
gethits: no visible global function definition for 'read.table'
normalizeGC: no visible global function definition for 'median'
plotCNOGpro: no visible global function definition for 'par'
plotCNOGpro: no visible global function definition for 'rainbow'
plotCNOGpro: no visible global function definition for 'density'
plotCNOGpro: no visible global function definition for 'polygon'
plotCNOGpro: no visible global function definition for 'lines'
plotCNOGpro: no visible global function definition for 'legend'
plotCNOGpro: no visible global function definition for 'boxplot'
sampleChromosome: no visible global function definition for 'median'
sampleChromosome: no visible binding for global variable 'var'
setupEmissionMatrix: no visible global function definition for 'dgeom'
store: no visible global function definition for 'write.table'
Undefined global functions or variables:
  boxplot density dgeom legend lines median par polygon quantile
  rainbow read.table setTxtProgressBar txtProgressBar var write.table
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "boxplot", "legend", "lines", "par", "polygon")
  importFrom("stats", "density", "dgeom", "median", "quantile", "var")
  importFrom("utils", "read.table", "setTxtProgressBar",
             "txtProgressBar", "write.table")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'latticeExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
CNclusterNcenter: no visible global function definition for 'median'
CNclusterNcenter: no visible binding for global variable 'var'
breakIntoGaps: no visible global function definition for 'runif'
centerprob: no visible global function definition for 'pnorm'
getz: no visible global function definition for 'predict'
smad: no visible global function definition for 'mad'
smedian: no visible global function definition for 'median'
smedian.sample: no visible global function definition for 'median'
smedmad: no visible global function definition for 'median'
smedmad: no visible global function definition for 'mad'
Undefined global functions or variables:
  mad median pnorm predict runif var
Consider adding
  importFrom("stats", "mad", "median", "pnorm", "predict", "runif",
             "var")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/CNull/CNull.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cnum/cnum.Rcheck/00install.out' for details.
Packages required but not available:
  'rstan', 'rstantools', 'RcppParallel', 'StanHeaders'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'GenomicInteractions', 'OpenImageR', 'biomaRt', 'rtracklayer'

Packages suggested but not available for checking:
  'ComplexHeatmap', 'igraph', 'GenomicFeatures',
  'BSgenome.Hsapiens.UCSC.hg19'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'twang'
Package unavailable to check Rd xrefs: 'twang'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/COBRA/COBRA.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cobs/cobs.Rcheck/00install.out' for details.
Namespaces in Imports field not imported from:
  'Matrix' 'nnet'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Note: found 14729 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package which this enhances but not available for checking: 'rkward'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package which this enhances but not available for checking: 'rkward'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/coda.base/coda.base.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/codadiags/codadiags.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking:
  'shinytest', 'roxygen2', 'ufs', 'userfriendlyscience'
Namespaces in Imports field not imported from:
  'graphics' 'jsonlite' 'rlang' 'tidyselect' 'vctrs'
  All declared Imports should be used.
Note: found 65 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Note: found 30244 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'XML'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Note: found 6 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/codep/codep.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'kableExtra'

Package suggested but not available for checking: 'devtools'

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

Package suggested but not available for checking: 'wTO'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'devtools'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/coenoflex/coenoflex.Rcheck/00install.out' for details.
Malformed Description field: should contain one or more complete sentences.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'tibble'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/coga/coga.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'paws'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'DiagrammeR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
BMDE: no visible global function definition for 'quantile'
BMDU: no visible global function definition for 'runif'
BMDU: no visible global function definition for 'quantile'
FS: no visible global function definition for 'qnorm'
GM: no visible global function definition for 'qchisq'
QH: no visible global function definition for 'qchisq'
SG : sgp: no visible global function definition for 'ppois'
SG : sgp: no visible global function definition for 'dpois'
WALD: no visible global function definition for 'qchisq'
WALDCC: no visible global function definition for 'qchisq'
WS: no visible global function definition for 'qchisq'
Undefined global functions or variables:
  dpois ppois qchisq qnorm quantile runif
Consider adding
  importFrom("stats", "dpois", "ppois", "qchisq", "qnorm", "quantile",
             "runif")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespaces in Imports field not imported from:
  'Rdpack' 'coin' 'ggplot2' 'plyr'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/coin/coin.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'spelling'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cold/cold.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'sf', 'weights'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/collapse/collapse.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/collections/collections.Rcheck/00install.out' for details.
Note: found 4186 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/collpcm/collpcm.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/collUtils/collUtils.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'rgl'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'imager'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'vdiffr'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'png'
Error(s) in re-building vignettes:
--- re-building 'colorBlindness.Rmd' using rmarkdown
Warning: It is deprecated to specify `guide = FALSE` to remove a guide. Please use `guide = "none"` instead.
Quitting from lines 123-137 (colorBlindness.Rmd) 
Error: processing vignette 'colorBlindness.Rmd' failed with diagnostics:
there is no package called 'png'
--- failed re-building 'colorBlindness.Rmd'

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

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'jpeg', 'png'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
cICA: no visible global function definition for 'mvfft'
cICA: no visible global function definition for 'ar.yw'
cICA: no visible global function definition for 'rnorm'
scICA: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  ar.yw mvfft rnorm
Consider adding
  importFrom("stats", "ar.yw", "mvfft", "rnorm")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'pkgdown'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/colorednoise/colorednoise.Rcheck/00install.out' for details.
Packages required but not available: 'treemap', 'png', 'jpeg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Title field: should not end in a period.
Package in Depends field not imported from: 'grid'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
plotVenn2d : twoWayOverlap: no visible global function definition for
  'grid.polygon'
plotVenn2d : twoWayOverlap: no visible global function definition for
  'gpar'
plotVenn2d: no visible global function definition for 'grid.text'
plotVenn2d: no visible global function definition for 'gpar'
plotVenn2d: no visible global function definition for 'grid.polygon'
plotVenn3d : twoWayOverlap: no visible global function definition for
  'grid.polygon'
plotVenn3d : twoWayOverlap: no visible global function definition for
  'gpar'
plotVenn3d: no visible global function definition for 'grid.text'
plotVenn3d: no visible global function definition for 'gpar'
plotVenn3d: no visible global function definition for 'grid.polygon'
plotVenn4d : getCommonEllipse: no visible global function definition
  for 'aggregate'
plotVenn4d : region.polygon: no visible global function definition for
  'head'
plotVenn4d : region.polygon: no visible global function definition for
  'grid.polygon'
plotVenn4d : region.polygon: no visible global function definition for
  'gpar'
plotVenn4d: no visible global function definition for 'grid.text'
plotVenn4d: no visible global function definition for 'gpar'
plotVenn4d: no visible global function definition for 'pushViewport'
plotVenn4d: no visible global function definition for 'viewport'
plotVenn4d: no visible global function definition for 'grid.polygon'
plotVenn4d: no visible global function definition for 'upViewport'
resizeCircles: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  aggregate gpar grid.polygon grid.text head pushViewport uniroot
  upViewport viewport
Consider adding
  importFrom("stats", "aggregate", "uniroot")
  importFrom("utils", "head")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'rvest', 'xml2'

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:
  'sf', 'rnaturalearth', 'tigris'
Error(s) in re-building vignettes:
--- re-building 'introduction.Rmd' using rmarkdown
Quitting from lines 58-65 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'sf'
--- failed re-building 'introduction.Rmd'

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

--- re-building 'tuning.Rmd' using rmarkdown
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
--- finished re-building 'tuning.Rmd'

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

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Note: found 742 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
generateMonochromaticColors: no visible global function definition for
  'col2rgb'
generateMonochromaticColors: no visible global function definition for
  'rgb'
generateMonochromaticColors: no visible global function definition for
  'tail'
hsv2rgb: no visible global function definition for 'rgb'
rotational_dispersion: no visible global function definition for
  'col2rgb'
rotational_dispersion: no visible global function definition for
  'rgb2hsv'
tetradicColors: no visible global function definition for 'head'
triadicColors: no visible global function definition for 'head'
Undefined global functions or variables:
  col2rgb head rgb rgb2hsv tail
Consider adding
  importFrom("grDevices", "col2rgb", "rgb", "rgb2hsv")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespaces in Imports field not imported from:
  'grid' 'gridExtra'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Malformed Description field: should contain one or more complete sentences.
primary.colors: no visible global function definition for 'rgb'
rgb.tables: no visible global function definition for 'rgb'
ygobb: no visible global function definition for 'approx'
ygobb: no visible global function definition for 'rgb'
Undefined global functions or variables:
  approx rgb
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("stats", "approx")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'Hmisc'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'png', 'jpeg'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/colorspace/colorspace.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'rgl'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Malformed Description field: should contain one or more complete sentences.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'XML', 'png'

Package suggested but not available for checking: 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/colourvalues/colourvalues.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'rgl'
Error(s) in re-building vignettes:
--- re-building 'colourvision-vignette.Rmd' using rmarkdown
Quitting from lines 591-593 (colourvision-vignette.Rmd) 
Error: processing vignette 'colourvision-vignette.Rmd' failed with diagnostics:
there is no package called 'rgl'
--- failed re-building 'colourvision-vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'crayon'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'igraph', 'XML', 'clusterSim'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/comat/comat.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespaces in Imports field not imported from:
  'chi' 'dplyr' 'spatstat.utils' 'utils'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Malformed Description field: should contain one or more complete sentences.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'spelling'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
competitive.test: no visible global function definition for 'runif'
selfcontained.test : fun2: no visible global function definition for
  'qchisq'
selfcontained.test: no visible global function definition for 'cov'
selfcontained.test: no visible global function definition for 'qchisq'
selfcontained.test: no visible global function definition for 'cor'
selfcontained.test: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  cor cov pchisq qchisq runif
Consider adding
  importFrom("stats", "cor", "cov", "pchisq", "qchisq", "runif")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/combiter/combiter.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'rgl'
'library' or 'require' calls in package code:
  'lattice' 'rgl'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cometExactTest/cometExactTest.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'R6'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'rstudioapi'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'adespatial'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'xml2'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/commonmark/commonmark.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/Compack/Compack.Rcheck/00install.out' for details.
addxaxis: no visible global function definition for 'par'
addxaxis: no visible global function definition for 'axis'
addxaxis: no visible global function definition for 'mtext'
eplot: no visible global function definition for 'par'
eplot: no visible global function definition for 'axis'
eplot: no visible global function definition for 'mtext'
Undefined global functions or variables:
  axis mtext par
Consider adding
  importFrom("graphics", "axis", "mtext", "par")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/comparator/comparator.Rcheck/00install.out' for details.
Packages suggested but not available for checking:
  'pcalg', 'backShift', 'CAM', 'huge', 'flare'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/compareC/compareC.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'magrittr'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'kableExtra', 'flextable', 'officer'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'R6'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/compas/compas.Rcheck/00install.out' for details.
Namespaces in Imports field not imported from:
  'PearsonDS' 'VGAM' 'actuar' 'fExtremes' 'rmutil'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/comperank/comperank.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'ggplot2'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/compHclust/compHclust.Rcheck/00install.out' for details.
Packages required but not available: 'spdep', 'Hmisc', 'nonparaeff'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'vdiffr'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package in Depends field not imported from: 'numDeriv'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
dcomplnorm: no visible global function definition for 'grad'
dcomplnorm : f1: no visible global function definition for 'dlnorm'
dcomplnorm : F1: no visible global function definition for 'plnorm'
dcomplnorm : f1L: no visible global function definition for 'dlnorm'
dcomplnorm : F1L: no visible global function definition for 'plnorm'
pcomplnorm: no visible global function definition for 'grad'
pcomplnorm : f1: no visible global function definition for 'dlnorm'
pcomplnorm : F1: no visible global function definition for 'plnorm'
pcomplnorm : F1L: no visible global function definition for 'plnorm'
qcomplnorm: no visible global function definition for 'grad'
qcomplnorm : f1: no visible global function definition for 'dlnorm'
qcomplnorm : F1q: no visible global function definition for 'qlnorm'
qcomplnorm : F1: no visible global function definition for 'plnorm'
rcomplnorm: no visible global function definition for 'runif'
Undefined global functions or variables:
  dlnorm grad plnorm qlnorm runif
Consider adding
  importFrom("stats", "dlnorm", "plnorm", "qlnorm", "runif")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/CompModels/CompModels.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/COMPoissonReg/COMPoissonReg.Rcheck/00install.out' for details.
Package required but not available: 'Directional'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'rgl'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/compositions/compositions.Rcheck/00install.out' for details.
Packages required but not available: 'otsad', 'kableExtra'

Package suggested but not available for checking: 'rgdal'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to 'hypergeo' which was already attached by Depends.
  Please remove these calls from your code.
momentCompound: no visible global function definition for 'integrate'
pgfIhypergeometric: no visible global function definition for 'uniroot'
pgfIhyperpoisson: no visible global function definition for 'uniroot'
pgfIkattitypeh1: no visible global function definition for 'uniroot'
pgfIkattitypeh2: no visible global function definition for 'uniroot'
pgfIneymantypeb: no visible global function definition for 'uniroot'
pgfIneymantypec: no visible global function definition for 'uniroot'
pgfIpoissonlindley: no visible global function definition for 'uniroot'
pgfIthomas: no visible global function definition for 'uniroot'
pgfIwaring: no visible global function definition for 'uniroot'
pgfIyule: no visible global function definition for 'uniroot'
rCompound: no visible global function definition for 'runif'
Undefined global functions or variables:
  integrate runif uniroot
Consider adding
  importFrom("stats", "integrate", "runif", "uniroot")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/CompQuadForm/CompQuadForm.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/CompRandFld/CompRandFld.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'rvest', 'sf', 'xml2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
kef: no visible global function definition for 'dgamma'
kef: no visible global function definition for 'dlnorm'
simp_int: no visible global function definition for 'approx'
Undefined global functions or variables:
  approx dgamma dlnorm
Consider adding
  importFrom("stats", "approx", "dgamma", "dlnorm")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

Package suggested but not available for checking: 'tidyverse'

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.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ConConPiWiFun/ConConPiWiFun.Rcheck/00install.out' for details.
Note: found 92 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/concreg/concreg.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'flextable', 'officer', 'survminer'

Packages suggested but not available for checking:
  'roxygen2', 'spelling', 'rms', 'brms', 'rstan', 'rstanarm', 'vdiffr',
  'ggtext', 'daewr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
K1.norm: no visible global function definition for 'dnorm'
K1.norm: no visible global function definition for 'pnorm'
K1.t3: no visible global function definition for 'pt'
K2.norm: no visible global function definition for 'dnorm'
K2.norm: no visible global function definition for 'pnorm'
K2.t3: no visible global function definition for 'pt'
Undefined global functions or variables:
  dnorm pnorm pt
Consider adding
  importFrom("stats", "dnorm", "pnorm", "pt")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/condmixt/condmixt.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Malformed Description field: should contain one or more complete sentences.
ml_solver: no visible global function definition for 'approx'
select_kmax: no visible global function definition for 'median'
Undefined global functions or variables:
  approx median
Consider adding
  importFrom("stats", "approx", "median")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/condSURV/condSURV.Rcheck/00install.out' for details.
Packages suggested but not available for checking: 'roxygen2', 'spelling'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'keras', 'mlr'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/coneproj/coneproj.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'spelling'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'pkgdown'
Namespace in Imports field not imported from: 'memoise'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'xml2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'mvtnorm'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespaces in Imports field not imported from:
  'e1071' 'ggplot2' 'lattice' 'magrittr' 'mlbench' 'randomForest'
  'scales' 'tibble' 'tidyr'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking:
  'phangorn', 'Quartet', 'TreeSearch'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: 'graphics'
  All declared Imports should be used.
conicPlot: no visible global function definition for 'palette'
conicPlotAsymptotes: no visible global function definition for
  'palette'
conicPlotAsymptotes: no visible global function definition for 'abline'
conicPlotAxes: no visible global function definition for 'palette'
conicPlotAxes: no visible global function definition for 'abline'
plotDegenerateConic: no visible global function definition for 'points'
plotDegenerateConic: no visible global function definition for 'abline'
plotEllipsis: no visible global function definition for 'lines'
plotEllipsis: no visible global function definition for 'points'
plotHyperbola: no visible global function definition for 'lines'
plotHyperbola: no visible global function definition for 'points'
plotParabola: no visible global function definition for 'lines'
Undefined global functions or variables:
  abline lines palette points
Consider adding
  importFrom("grDevices", "palette")
  importFrom("graphics", "abline", "lines", "points")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Malformed Title field: should not end in a period.
'library' or 'require' call to 'parallel' which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  'Rmpi' 'snow'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'parallel'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ConjointChecks: no visible global function definition for 'makeCluster'
ConjointChecks: no visible global function definition for
  'clusterSetRNGStream'
ConjointChecks: no visible global function definition for
  'clusterApply'
ConjointChecks: no visible global function definition for 'stopCluster'
omni.check: no visible global function definition for 'runif'
omni.check: no visible global function definition for 'quantile'
plot.checks: no visible global function definition for 'mtext'
plot.checks: no visible global function definition for 'text'
Undefined global functions or variables:
  clusterApply clusterSetRNGStream makeCluster mtext quantile runif
  stopCluster text
Consider adding
  importFrom("graphics", "mtext", "text")
  importFrom("stats", "quantile", "runif")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'sf', 'lwgeom'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'lintr'
Namespaces in Imports field not imported from:
  'R6' 'httr' 'jsonlite'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'igraph'
Package unavailable to check Rd xrefs: 'igraph'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available:
  'igraph', 'ComplexHeatmap', 'leidenAlg', 'sccore'

Packages suggested but not available for checking:
  'AnnotationDbi', 'conosPanel', 'DESeq2', 'ggrastr', 'GO.db',
  'org.Hs.eg.db', 'org.Mm.eg.db', 'p2data', 'pagoda2', 'Seurat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/conquer/conquer.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/conquestr/conquestr.Rcheck/00install.out' for details.
Packages required but not available: 'rgdal', 'rnaturalearth', 'sf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'scales' 'sna'
  All declared Imports should be used.
Note: found 244 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'Gmisc'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'ConsRank', 'rlist'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ConsReg/ConsReg.Rcheck/00install.out' for details.
Packages suggested but not available for checking: 'units', 'quantities'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'devtools'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'spdep'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/constrainedKriging/constrainedKriging.Rcheck/00install.out' for details.
Packages required but not available: 'rstan', 'rstantools', 'StanHeaders'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'spelling'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'igraph', 'rgdal'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ContaminatedMixt/ContaminatedMixt.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'spelling'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'devtools', 'vdiffr'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/contfrac/contfrac.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/contoureR/contoureR.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'rms'

Package suggested but not available for checking: 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 3 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'SHELF'

Package suggested but not available for checking: 'spelling'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'eurostat'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available:
  'AnnotationDbi', 'org.Hs.eg.db', 'org.Mm.eg.db', 'biomaRt', 'xml2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'phytools', 'geiger'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'ClustGeo'

Package suggested but not available for checking: 'imager'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'rgl'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/coop/coop.Rcheck/00install.out' for details.
Packages required but not available: 'igraph', 'optrees'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/copCAR/copCAR.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'sf', 'gdalUtils'

Packages suggested but not available for checking:
  'fitbitViz', 'tmap', 'leaflet', 'leafgl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'smacof'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'rstan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'cec2005benchmark'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/copula/copula.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/coRanking/coRanking.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

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

Package suggested but not available for checking: 'Cairo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'mcc'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cord/cord.Rcheck/00install.out' for details.
Package required but not available: 'igraph'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/CORElearn/CORElearn.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/corels/corels.Rcheck/00install.out' for details.
Package required but not available: 'XML'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
advanceRNG: no visible global function definition for 'runif'
randomEventMoves: no visible global function definition for 'runif'
randomRescaledEventMoves: no visible global function definition for
  'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Malformed Description field: should contain one or more complete sentences.
coreTDT_geneset: no visible global function definition for
  'write.table'
pvalue_calculator: no visible global function definition for 'dbinom'
Undefined global functions or variables:
  dbinom write.table
Consider adding
  importFrom("stats", "dbinom")
  importFrom("utils", "write.table")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'phangorn', 'igraph', 'phytools'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
compute.llh: no visible global function definition for 'dnorm'
compute.u.hat.simple: no visible global function definition for 'dnorm'
fit.CLM.1u.simple.start: no visible global function definition for
  'kmeans'
fit.CLMM.simple.start: no visible global function definition for
  'kmeans'
fit.CLMM.simple.start.NA: no visible global function definition for
  'kmeans'
Undefined global functions or variables:
  dnorm kmeans
Consider adding
  importFrom("stats", "dnorm", "kmeans")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'phyloseq'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'roxygen2'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(CornerstoneR)
  > 
  > test_check("CornerstoneR")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_misc.R:18:3): Internal Version ──────────────────────────────────
  Error: there is no package called 'xml2'
  Backtrace:
      █
   1. ├─utils::news(package = "CornerstoneR") test_misc.R:18:2
   2. │ └─tools:::.build_news_db(package, lib.loc, format, reader)
   3. │   └─tools:::.build_news_db_from_package_NEWS_md(nfile)
   4. └─base::loadNamespace(x)
   5.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   6.     └─base:::withOneRestart(expr, restarts[[1L]])
   7.       └─base:::doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 339 ]
  Error: Test failures
  Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'devtools'

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
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'shinytest'
Namespaces in Imports field not imported from:
  'RColorBrewer' 'ggplot2' 'rmarkdown' 'shinyWidgets' 'shinydashboard'
  'shinyjs'
  All declared Imports should be used.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(corporaexplorer)
  > 
  > test_check("corporaexplorer")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_explorer_app.R:4:1): (code run outside of `test_that()`) ────────
  Error: there is no package called 'shinytest'
  Backtrace:
      █
   1. └─base::library(shinytest) test_explorer_app.R:4:0
  ── Error (test_extractor_app.R:4:1): (code run outside of `test_that()`) ───────
  Error: there is no package called 'shinytest'
  Backtrace:
      █
   1. └─base::library(shinytest) test_extractor_app.R:4:0
  
  [ FAIL 2 | WARN 1 | SKIP 0 | PASS 1 ]
  Error: Test failures
  Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Note: found 1187 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages which this enhances but not available for checking:
  'quanteda', 'tm'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/corpus/corpus.Rcheck/00install.out' for details.
Packages required but not available:
  'quanteda', 'igraph', 'RNewsflow', 'rsyntax'

Packages suggested but not available for checking: 'tm', 'topicmodels'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'rgl'
Namespaces in Imports field not imported from:
  'profr' 'xtable'
  All declared Imports should be used.
Package unavailable to check Rd xrefs: 'rgl'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/CorrBin/CorrBin.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'XML'

Package suggested but not available for checking: 'xcms'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'utils'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking:
  'Hmisc', 'rstanarm', 'spelling'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'spelling'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'sparklyr'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
corr.Qmatrix: no visible global function definition for 'cor'
corr.Qmatrix: no visible global function definition for 'cor.test'
summarise.Fst: no visible global function definition for 'cor'
summarise.Fst: no visible global function definition for 'sd'
summarise.lnPD: no visible global function definition for 'sd'
Undefined global functions or variables:
  cor cor.test sd
Consider adding
  importFrom("stats", "cor", "cor.test", "sd")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
dist: no visible global function definition for 'quantile'
edgecount: no visible global function definition for 'reshape'
edgecutoff: no visible global function definition for 'boxplot'
edgecutoff: no visible global function definition for 'sd'
edgecutoff: no visible global function definition for 'median'
edgecutoff: no visible global function definition for 'IQR'
Undefined global functions or variables:
  IQR boxplot median quantile reshape sd
Consider adding
  importFrom("graphics", "boxplot")
  importFrom("stats", "IQR", "median", "quantile", "reshape", "sd")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespaces in Imports field not imported from:
  'knitr' 'rmarkdown'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'spelling'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cort/cort.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Malformed Description field: should contain one or more complete sentences.
GA_search : subset_score: no visible global function definition for
  'combn'
choose_lambda : subset_score: no visible global function definition for
  'combn'
cond.fyx: no visible global function definition for 'var'
cond.fyx: no visible global function definition for 'cor'
diff_gen_PPI: no visible global function definition for 'cov'
diff_gen_PPI: no visible global function definition for 'sd'
f.test: no visible binding for global variable 'var'
get_quantiles : node_edge: no visible global function definition for
  'combn'
score_scaling: no visible global function definition for 'hist'
score_scaling: no visible global function definition for 'sd'
Undefined global functions or variables:
  combn cor cov hist sd var
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "cor", "cov", "sd", "var")
  importFrom("utils", "combn")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
cosinor.lm: no visible binding for global variable 'na.omit'
cosinor.lm: no visible global function definition for 'terms'
cosinor.lm: no visible global function definition for 'as.formula'
cosinor.lm: no visible global function definition for 'lm'
cosinor_analyzer: no visible binding for global variable 'vitamind'
cosinor_analyzer : <anonymous>: no visible global function definition
  for 'as.formula'
ggplot.cosinor.lm: no visible global function definition for 'predict'
predict.cosinor.lm: no visible global function definition for 'fitted'
predict.cosinor.lm: no visible global function definition for 'predict'
simulate_cosinor: no visible global function definition for 'runif'
simulate_cosinor: no visible global function definition for 'rbinom'
simulate_cosinor: no visible global function definition for 'rnorm'
summary.cosinor.lm: no visible global function definition for 'vcov'
summary.cosinor.lm: no visible global function definition for 'qnorm'
summary.cosinor.lm: no visible global function definition for 'pnorm'
test_cosinor: no visible global function definition for 'pchisq'
test_cosinor: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  as.formula fitted lm na.omit pchisq pnorm predict qnorm rbinom rnorm
  runif terms vcov vitamind
Consider adding
  importFrom("stats", "as.formula", "fitted", "lm", "na.omit", "pchisq",
             "pnorm", "predict", "qnorm", "rbinom", "rnorm", "runif",
             "terms", "vcov")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Malformed Title field: should not end in a period.
D.M: no visible global function definition for 'integrate'
lookbackTime: no visible global function definition for 'integrate'
Undefined global functions or variables:
  integrate
Consider adding
  importFrom("stats", "integrate")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Malformed Title field: should not end in a period.
Packages in Depends field not imported from:
  'Rglpk' 'glmnet' 'parallel' 'quadprog'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/costsensitive/costsensitive.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'OpenMx', 'ctsem', 'MBESS', 'scholar'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'colordistance', 'png', 'jpeg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/countdata/countdata.Rcheck/00install.out' for details.
Package required but not available: 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'spelling'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/Countr/Countr.Rcheck/00install.out' for details.
Note: found 128401 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'ComplexHeatmap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'dataRetrieval'

Package suggested but not available for checking: 'hurricaneexposure'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'choroplethr'
Error(s) in re-building vignettes:
--- re-building 'countytimezones.Rmd' using rmarkdown
Quitting from lines 111-123 (countytimezones.Rmd) 
Error: processing vignette 'countytimezones.Rmd' failed with diagnostics:
there is no package called 'choroplethr'
--- failed re-building 'countytimezones.Rmd'

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

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/COUSCOus/COUSCOus.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/covafillr/covafillr.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'gstat'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/covBM/covBM.Rcheck/00install.out' for details.
Packages suggested but not available for checking: 'qgraph', 'igraph'
Error(s) in re-building vignettes:
--- re-building 'CovCombR.rmd' using rmarkdown
Quitting from lines 66-68 (CovCombR.rmd) 
Error: processing vignette 'CovCombR.rmd' failed with diagnostics:
there is no package called 'qgraph'
--- failed re-building 'CovCombR.rmd'

SUMMARY: processing the following file failed:
  'CovCombR.rmd'

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespaces in Imports field not imported from:
  'colourpicker' 'dplyr' 'markdown' 'shinyjs' 'table1' 'tidyr'
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building 'Exposure_Response_Example.Rmd' using rmarkdown
Building exprespmodel ... error.
Warning message:
In system(cmd) : 'make' not foundQuitting from lines 56-102 (Exposure_Response_Example.Rmd) 
Error: processing vignette 'Exposure_Response_Example.Rmd' failed with diagnostics:
the model build step failed.
--- failed re-building 'Exposure_Response_Example.Rmd'

--- re-building 'Introduction_to_coveffectsplot.Rmd' using rmarkdown
Picking joint bandwidth of 0.0273
Picking joint bandwidth of 0.0326
Warning: Removed 57 rows containing non-finite values (stat_density).
--- finished re-building 'Introduction_to_coveffectsplot.Rmd'

--- re-building 'PKPD_Example.Rmd' using rmarkdown
Building codepkpdmodelcov ... error.
Warning message:
In system(cmd) : 'make' not foundQuitting from lines 67-138 (PKPD_Example.Rmd) 
Error: processing vignette 'PKPD_Example.Rmd' failed with diagnostics:
the model build step failed.
--- failed re-building 'PKPD_Example.Rmd'

--- re-building 'PK_Example.Rmd' using rmarkdown
Building codepkmodelcov ... error.
Warning message:
In system(cmd) : 'make' not foundQuitting from lines 62-109 (PK_Example.Rmd) 
Error: processing vignette 'PK_Example.Rmd' failed with diagnostics:
the model build step failed.
--- failed re-building 'PK_Example.Rmd'

--- re-building 'Pediatric_Cov_Sim.Rmd' using rmarkdown
Building pedpkmodelcov ... error.
Warning message:
In system(cmd) : 'make' not foundQuitting from lines 45-115 (Pediatric_Cov_Sim.Rmd) 
Error: processing vignette 'Pediatric_Cov_Sim.Rmd' failed with diagnostics:
the model build step failed.
--- failed re-building 'Pediatric_Cov_Sim.Rmd'

SUMMARY: processing the following files failed:
  'Exposure_Response_Example.Rmd' 'PKPD_Example.Rmd' 'PK_Example.Rmd'
  'Pediatric_Cov_Sim.Rmd'

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/covglasso/covglasso.Rcheck/00install.out' for details.
Package required but not available: 'rentrez'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'tidyverse'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'networkD3'
Error(s) in re-building vignettes:
--- re-building 'covid19dbcand.Rmd' using rmarkdown
Quitting from lines 78-190 (covid19dbcand.Rmd) 
Error: processing vignette 'covid19dbcand.Rmd' failed with diagnostics:
there is no package called 'networkD3'
--- failed re-building 'covid19dbcand.Rmd'

SUMMARY: processing the following file failed:
  'covid19dbcand.Rmd'

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'lubridate'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'devtools', 'mapview', 'sf'

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.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'sf'

Package suggested but not available for checking: 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'tidyverse'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'xml2'

Packages suggested but not available for checking:
  'ggspatial', 'pkgdown', 'rvest', 'sf', 'spelling'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'devtools'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'library' or 'require' calls to packages already attached by Depends:
  'Matrix' 'mlogit' 'poLCA'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'Matrix' 'mlogit' 'poLCA'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
covLCA: no visible global function definition for 'model.response'
covLCA: no visible global function definition for 'model.frame'
covLCA: no visible global function definition for 'model.matrix'
covLCA: no visible global function definition for 'rnorm'
covLCA: no visible global function definition for 'flush.console'
covLCA: no visible global function definition for 'ginv'
covLCA.initialAlphaGamma: no visible global function definition for
  'as.formula'
covLCA.initialAlphaGamma: no visible global function definition for
  'mlogit.data'
covLCA.initialAlphaGamma: no visible global function definition for
  'mlogit'
covLCA.initialBeta: no visible global function definition for
  'as.formula'
covLCA.initialBeta: no visible global function definition for 'poLCA'
covLCA.initialBeta: no visible global function definition for
  'mlogit.data'
covLCA.initialBeta: no visible global function definition for 'mlogit'
covLCA.paramVariance: no visible global function definition for 'ginv'
covLCA.varianceFirst: no visible global function definition for 'bdiag'
Undefined global functions or variables:
  as.formula bdiag flush.console ginv mlogit mlogit.data model.frame
  model.matrix model.response poLCA rnorm
Consider adding
  importFrom("stats", "as.formula", "model.frame", "model.matrix",
             "model.response", "rnorm")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
covreg.mcmc: no visible global function definition for 'model.frame'
covreg.mcmc: no visible global function definition for 'model.matrix'
covreg.mcmc: no visible global function definition for 'model.response'
covreg.mcmc: no visible global function definition for 'lm'
covreg.mcmc: no visible global function definition for 'rnorm'
covreg.mcmc: no visible global function definition for 'cov'
rmn: no visible global function definition for 'rnorm'
rwish: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  cov lm model.frame model.matrix model.response rnorm
Consider adding
  importFrom("stats", "cov", "lm", "model.frame", "model.matrix",
             "model.response", "rnorm")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'xml2'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/covr/covr.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespaces in Imports field not imported from:
  'Rcpp' 'gsl'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/covTestR/covTestR.Rcheck/00install.out' for details.
Packages required but not available: 'shapes', 'SHT'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'Cairo', 'vdiffr'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'rms', 'mediation'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/coxinterval/coxinterval.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/coxme/coxme.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/coxphf/coxphf.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/coxphw/coxphw.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/CoxPlus/CoxPlus.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/coxrobust/coxrobust.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/coxrt/coxrt.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/coxsei/coxsei.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package in Depends field not imported from: 'tcltk'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'tikzDevice'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/CPAT/CPAT.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cPCG/cPCG.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'rms'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/CPGLIB/CPGLIB.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cplm/cplm.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cpm/cpm.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'RcppParallel'

Package suggested but not available for checking: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'rgl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cpss/cpss.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'rvest', 'xml2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'leaflet'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'introduction.Rmd' using rmarkdown
Quitting from lines 399-421 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'leaflet'
--- failed re-building 'introduction.Rmd'

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

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cqrReg/cqrReg.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
distance.comoving: no visible global function definition for
  'integrate'
Undefined global functions or variables:
  integrate
Consider adding
  importFrom("stats", "integrate")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'xml2', 'rvest', 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(cranlike)
  > 
  > test_check("cranlike")
  /bin/sh: line 1: gzip: command not found
  /usr/bin/tar: Child returned status 127
  /usr/bin/tar: Error is not recoverable: exiting now
  /bin/sh: line 1: gzip: command not found
  /usr/bin/tar: Child returned status 127
  /usr/bin/tar: Error is not recoverable: exiting now
  /bin/sh: line 1: gzip: command not found
  /usr/bin/tar: Child returned status 127
  /usr/bin/tar: Error is not recoverable: exiting now
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-edge-cases.R:121:3): DESCRIPTION missing required fields ──────
  `update_PACKAGES(dir2)` produced unexpected warnings.
  Expected match: No version number
  Actual values:
  * Cannot extract valid DESCRIPTION, 'C:\msys64\home\tomas\ucrt3\svn\ucrt3\r_packages\pkgcheck\CRAN\cranlike\tmp\Rtmpwjuq9M\file41641573167\pkg_1.0.0.tar.gz' will be ignored is.character(keys) is not TRUE
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 78 ]
  Error: Test failures
  Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'igraph', 'tm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 11 marked Latin-1 strings
  Note: found 57 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Malformed Description field: should contain one or more complete sentences.
crantastic.submitInstalledPackages: no visible global function
  definition for 'installed.packages'
postData: no visible global function definition for 'make.socket'
postData: no visible global function definition for 'write.socket'
postData: no visible global function definition for 'read.socket'
postData: no visible global function definition for 'close.socket'
Undefined global functions or variables:
  close.socket installed.packages make.socket read.socket write.socket
Consider adding
  importFrom("utils", "close.socket", "installed.packages",
             "make.socket", "read.socket", "write.socket")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'gdistance', 'rmapshaper', 'sf'

Package suggested but not available for checking: 'rgdal'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/crch/crch.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/crctStepdown/crctStepdown.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Malformed Description field: should contain one or more complete sentences.
cm.CVaR: no visible global function definition for 'quantile'
cm.hist: no visible global function definition for 'hist'
cm.quantile: no visible global function definition for 'qnorm'
cm.rnorm: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  hist qnorm quantile rnorm
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "qnorm", "quantile", "rnorm")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'pmml', 'XML'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/credule/credule.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

Packages suggested but not available for checking:
  'AnnotationDbi', 'org.Hs.eg.db', 'clusterProfiler'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/CRF/CRF.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/crfsuite/crfsuite.Rcheck/00install.out' for details.
Package required but not available: 'XML'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/crimCV/crimCV.Rcheck/00install.out' for details.
Package required but not available: 'sf'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'spelling'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'rtracklayer'

Package suggested but not available for checking: 'BSgenome.Scerevisiae.UCSC.sacCer2'

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

Package suggested but not available for checking: 'DiagrammeR'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/CRM/CRM.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'library' or 'require' call to 'RCurl' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'RCurl' 'chron'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
collateDaily: no visible global function definition for 'read.table'
collateDaily: no visible global function definition for 'write.table'
collateHourly: no visible global function definition for 'read.table'
collateHourly: no visible global function definition for 'write.table'
downloadCRN: no visible global function definition for 'download.file'
getUrlsCRN: no visible global function definition for 'getURL'
writeDataset: no visible global function definition for 'read.table'
writeDataset: no visible global function definition for 'write.table'
Undefined global functions or variables:
  download.file getURL read.table write.table
Consider adding
  importFrom("utils", "download.file", "read.table", "write.table")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Note: found 3 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'rgdal'

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

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

> ### Name: cumulative
> ### Title: Sum of a weather variable between between two dates
> ### Aliases: cumulative
> 
> ### ** Examples
> 
> ## Selected calculations
> library(tidyverse)
Error in library(tidyverse) : there is no package called 'tidyverse'
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(purrr)
  > library(testthat)
  
  Attaching package: 'testthat'
  
  The following object is masked from 'package:purrr':
  
      is_null
  
  > library(tidyverse)
  Error in library(tidyverse) : there is no package called 'tidyverse'
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'crop-grow-days.Rmd' using rmarkdown
Quitting from lines 28-31 (./../man/fragments/intro.Rmd) 
Quitting from lines 28-31 (./../man/fragments/intro.Rmd) 
Error: processing vignette 'crop-grow-days.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'crop-grow-days.Rmd'

--- re-building 'getting-weather-data.Rmd' using rmarkdown
Quitting from lines 28-31 (./../man/fragments/intro.Rmd) 
Quitting from lines 28-31 (./../man/fragments/intro.Rmd) 
Error: processing vignette 'getting-weather-data.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'getting-weather-data.Rmd'

SUMMARY: processing the following files failed:
  'crop-grow-days.Rmd' 'getting-weather-data.Rmd'

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'sf'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
get.plan: no visible global function definition for 'menu'
Undefined global functions or variables:
  menu
Consider adding
  importFrom("utils", "menu")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'nbpMatching'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/Crossover/Crossover.Rcheck/00install.out' for details.
BootC : BSs: no visible global function definition for 'lm'
BootC : BSs: no visible global function definition for 'vcov'
BootC: no visible global function definition for 'boot'
BootC: no visible global function definition for 'boot.ci'
DeltaC: no visible global function definition for 'lm'
DeltaC: no visible global function definition for 'vcov'
FiellerC: no visible global function definition for 'lm'
FiellerC: no visible global function definition for 'vcov'
nonLinearC: no visible global function definition for 'nls'
Undefined global functions or variables:
  boot boot.ci lm nls vcov
Consider adding
  importFrom("stats", "lm", "nls", "vcov")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'flextable', 'officer'

Packages suggested but not available for checking: 'xml2', 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespaces in Imports field not imported from:
  'R6' 'dplyr' 'r6extended'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'spelling', 'vdiffr'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/crqa/crqa.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/crrp/crrp.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/crrSC/crrSC.Rcheck/00install.out' for details.
crrstep : crr.makecov1: no visible global function definition for
  'model.matrix'
crrstep : crr.dropterm: no visible global function definition for
  'terms'
crrstep : crr.dropterm: no visible global function definition for
  'as.formula'
crrstep : crr.addterm: no visible global function definition for
  'terms'
crrstep : crr.addterm: no visible global function definition for
  'as.formula'
crrstep: no visible global function definition for 'as.formula'
crrstep: no visible global function definition for 'terms'
crrstep: no visible global function definition for 'model.frame'
crrstep: no visible binding for global variable 'na.pass'
crrstep: no visible global function definition for 'update'
crrstep: no visible global function definition for 'drop.terms'
Undefined global functions or variables:
  as.formula drop.terms model.frame model.matrix na.pass terms update
Consider adding
  importFrom("stats", "as.formula", "drop.terms", "model.frame",
             "model.matrix", "na.pass", "terms", "update")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'spelling'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Note: found 500 marked UTF-8 strings
Running examples in 'crsra-Ex.R' failed
The error most likely occurred in:

> ### Name: crsra_import_course
> ### Title: Imports all the .csv files into one list consisting of all the
> ###   tables within the course.
> ### Aliases: crsra_import_course
> 
> ### ** Examples
> 
> zip_file = system.file("extdata", "fake_course_7051862327916.zip",
+ package = "crsra")
> bn = basename(zip_file)
> bn = sub("[.]zip$", "", bn)
> res = unzip(zip_file, exdir = tempdir(), overwrite = TRUE)
Error in unzip(zip_file, exdir = tempdir(), overwrite = TRUE) : 
  cannot open file 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/crsra/tmp/RtmpYr66ab/fake_course_7051862327916/programming_submission_part_grid_grading_statuses.csv': Invalid argument
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'rgl'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/crs/crs.Rcheck/00install.out' for details.
Packages required but not available: 'sf', 'units', 'mapview'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'roxygen2'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking:
  'devtools', 'lintr', 'spelling'
Running 'spelling.R'
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > spelling::spell_check_test(
  +     vignettes = TRUE, error = identical(Sys.getenv("GITHUB_ACTION"), "true")
  + )
  Error in loadNamespace(x) : there is no package called 'spelling'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'shinytest', 'spelling'
Running 'spelling.R'
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
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'marmap', 'swfscDAS'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/CrypticIBDcheck/CrypticIBDcheck.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'spelling'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'qte'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'rms', 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'Rdpack'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'tm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespaces in Imports field not imported from:
  'extrafont' 'future'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'sf', 'rmapshaper'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Note: found 3 marked Latin-1 strings
  Note: found 55 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'ggraph', 'igraph'
Error(s) in re-building vignettes:
--- re-building 'cspp-vignette.Rmd' using rmarkdown
Please cite:

Caleb Lucas and Joshua McCrain (2020). cspp: A Package for The Correlates of State Policy Project Data.
R package version 0.3.1.

Jordan, Marty P. and Matt Grossmann. 2020. The Correlates of State Policy Project v.2.2.
East Lansing, MI: Institute for Public Policy and Social Research (IPPSR).

You are using version 2.2 of the CSPP data.

Quitting from lines 288-302 (cspp-vignette.Rmd) 
Error: processing vignette 'cspp-vignette.Rmd' failed with diagnostics:
there is no package called 'ggraph'
--- failed re-building 'cspp-vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
pielou: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package in Depends field not imported from: 'compiler'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
csSAM: no visible binding for global variable 'quantile'
csSAM: no visible global function definition for 'median'
csfit: no visible global function definition for 'lsfit'
csfit: no visible global function definition for 'ls.diag'
plotCsSAM: no visible global function definition for 'pdf'
plotCsSAM: no visible global function definition for 'par'
plotCsSAM: no visible global function definition for 'title'
plotCsSAM: no visible global function definition for 'dev.off'
runSAM: no visible binding for global variable 'median'
runSAM: no visible global function definition for 'quantile'
Undefined global functions or variables:
  dev.off ls.diag lsfit median par pdf quantile title
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "par", "title")
  importFrom("stats", "ls.diag", "lsfit", "median", "quantile")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cstab/cstab.Rcheck/00install.out' for details.
Malformed Title field: should not end in a period.
cstar: no visible global function definition for 'vcov'
cstar : utility: no visible global function definition for 'dt'
cstar : maximand: no visible global function definition for 'integrate'
cstar: no visible global function definition for 'uniroot'
cstari : utility: no visible global function definition for 'dt'
cstari : maximand: no visible global function definition for
  'integrate'
cstari: no visible global function definition for 'uniroot'
cstarme : utility: no visible global function definition for 'density'
cstarme : maximand: no visible global function definition for
  'integrate'
cstarme : maximand: no visible global function definition for 'sd'
cstarme: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  density dt integrate sd uniroot vcov
Consider adding
  importFrom("stats", "density", "dt", "integrate", "sd", "uniroot",
             "vcov")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/CSTE/CSTE.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/CSTools/CSTools.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/csvread/csvread.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Running 'test-all.R'
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library("testthat")
  > library("csvy")
  > test_check("csvy", reporter = "summary")
  metadata: 
  CSVY import/export with additional metadata: ....
  External metadata can be found and loaded: W.1.2
  read_metadata: ......
  read_csvy: 
  CSVY import using read_csvy(): .....
  write_csvy: 
  CSVY export using write_csvy(): .....
  write_metadata: 
  write_metadata: ............
  
  ══ Warnings ════════════════════════════════════════════════════════════════════
  1. External metadata loads automatically (test-metadata.R:43:5) - 'metadata' should be either a .json or .yaml file.
  
  ══ Failed ══════════════════════════════════════════════════════════════════════
  ── 1. Failure (test-metadata.R:45:5): External metadata loads automatically ────
  file.exists(tmp_metadata) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  ── 2. Error (test-metadata.R:48:5): External metadata loads automatically ──────
  Error: invalid 'description' argument
  Backtrace:
   1. testthat::expect_identical(...) test-metadata.R:48:4
   4. base::readLines(dir(dirname(tmp), pattern = ".yaml", full.names = TRUE))
   5. base::file(con, "r")
  
  ══ DONE ════════════════════════════════════════════════════════════════════════
  Error: Test failures
  Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespaces in Imports field not imported from:
  'epitools' 'rpivotTable' 'shinyMatrix'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

Package suggested but not available for checking: 'huge'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'roxygen2'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ctgt/ctgt.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ctl/ctl.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'markovchain'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ctmcd/ctmcd.Rcheck/00install.out' for details.
Package required but not available: 'gdistance'

Package suggested but not available for checking: 'crawl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'rgdal'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'Gmisc'

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

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

Package suggested but not available for checking: 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'ctsem', 'OpenMx'

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

Package suggested but not available for checking: 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'caret' 'datasets' 'dplyr' 'e1071' 'party' 'rhandsontable' 'rpart'
  'rpart.plot' 'shiny'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespaces in Imports field not imported from:
  'caret' 'datasets' 'dplyr' 'e1071' 'party' 'rhandsontable' 'rpart'
  'rpart.plot' 'shiny'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'XML'
Running examples in 'ctv-Ex.R' failed
The error most likely occurred in:

> ### Name: ctv-server
> ### Title: CRAN Task Views: Tools for Maintainers
> ### Aliases: read.ctv ctv2html check_ctv_packages repos_update_views
> ### Keywords: utilities
> 
> ### ** Examples
> 
> ## read .ctv file
> x <- read.ctv(system.file("ctv", "Econometrics.ctv", package = "ctv"))
Error in loadNamespace(x) : there is no package called 'XML'
Calls: read.ctv ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running 'read-all.R'
Running the tests in 'tests/read-all.R' failed.
Complete output:
  > #### Read all CTVs in the package:
  > 
  > library("ctv")
  > 
  > cdir <- system.file("ctv", package="ctv")
  > ctvs <- list.files(cdir, pattern = "\\.ctv$")
  > ctvs
   [1] "Bayesian.ctv"                  "ChemPhys.ctv"                 
   [3] "ClinicalTrials.ctv"            "Cluster.ctv"                  
   [5] "DifferentialEquations.ctv"     "Distributions.ctv"            
   [7] "Econometrics.ctv"              "Environmetrics.ctv"           
   [9] "ExperimentalDesign.ctv"        "ExtremeValue.ctv"             
  [11] "Finance.ctv"                   "FunctionalData.ctv"           
  [13] "Genetics.ctv"                  "Graphics.ctv"                 
  [15] "HighPerformanceComputing.ctv"  "MachineLearning.ctv"          
  [17] "MedicalImaging.ctv"            "MetaAnalysis.ctv"             
  [19] "ModelDeployment.ctv"           "Multivariate.ctv"             
  [21] "NaturalLanguageProcessing.ctv" "NumericalMathematics.ctv"     
  [23] "OfficialStatistics.ctv"        "Optimization.ctv"             
  [25] "Pharmacokinetics.ctv"          "Phylogenetics.ctv"            
  [27] "Psychometrics.ctv"             "ReproducibleResearch.ctv"     
  [29] "Robust.ctv"                    "SocialSciences.ctv"           
  [31] "Spatial.ctv"                   "SpatioTemporal.ctv"           
  [33] "Survival.ctv"                  "TimeSeries.ctv"               
  [35] "WebTechnologies.ctv"           "gR.ctv"                       
  > 
  > rr <- sapply(ctvs,
  + 	     function(ctv) {
  + 		 cat(sprintf("%25s  ",ctv))
  + 		 R <- read.ctv(file.path(cdir, ctv))
  + 		 cat("[ok]\n")
  +                  R
  + 	     },
  + 	     simplify=FALSE)
               Bayesian.ctv  Error in loadNamespace(x) : there is no package called 'XML'
  Calls: sapply ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Errors in running code in vignettes:
when running code in 'ctv-howto.Rnw'

> library("ctv")

> x <- read.ctv(system.file("ctv", "Econometrics.ctv", 
+     package = "ctv"))

  When sourcing 'ctv-howto.R':
Error: there is no package called 'XML'
Execution halted

  'ctv-howto.Rnw'... failed
Error(s) in re-building vignettes:
--- re-building 'ctv-howto.Rnw' using Sweave

Error: processing vignette 'ctv-howto.Rnw' failed with diagnostics:
 chunk 1 
Error in loadNamespace(x) : there is no package called 'XML'

--- failed re-building 'ctv-howto.Rnw'

SUMMARY: processing the following file failed:
  'ctv-howto.Rnw'

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cubature/cubature.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'stars'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cubfits/cubfits.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cubicBsplines/cubicBsplines.Rcheck/00install.out' for details.
Package required but not available: 'rgl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/Cubist/Cubist.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'spelling'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/curl/curl.Rcheck/00install.out' for details.
cci.nostrat: no visible global function definition for 'quantile'
cci.nostrat: no visible global function definition for 'axis'
cci.nostrat: no visible global function definition for 'lines'
cci.nostrat: no visible global function definition for 'legend'
cci.strat: no visible global function definition for 'axis'
cci.strat: no visible global function definition for 'lines'
cci.strat: no visible global function definition for 'legend'
clfs.nostrat: no visible global function definition for 'quantile'
clfs.nostrat: no visible global function definition for 'axis'
clfs.nostrat: no visible global function definition for 'lines'
clfs.nostrat: no visible global function definition for 'legend'
clfs.strat: no visible global function definition for 'axis'
clfs.strat: no visible global function definition for 'lines'
clfs.strat: no visible global function definition for 'legend'
pvals.2cat: no visible global function definition for 'pchisq'
pvals.cat: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  axis legend lines pchisq quantile
Consider adding
  importFrom("graphics", "axis", "legend", "lines")
  importFrom("stats", "pchisq", "quantile")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Note: found 459 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/curstatCI/curstatCI.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/curveDepth/curveDepth.Rcheck/00install.out' for details.
Package required but not available: 'rgl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cusp/cusp.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespaces in Imports field not imported from:
  'rlang' 'tidyselect'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/CUSUMdesign/CUSUMdesign.Rcheck/00install.out' for details.
Package which this enhances but not available for checking: 'vdiffr'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cusum/cusum.Rcheck/00install.out' for details.
Packages required but not available: 'set', 'do'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Cut: no visible global function definition for 'cor'
MissSimulation: no visible global function definition for 'rbinom'
cutoff: no visible global function definition for 'cor'
Undefined global functions or variables:
  cor rbinom
Consider adding
  importFrom("stats", "cor", "rbinom")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cutpointr/cutpointr.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Malformed Description field: should contain one or more complete sentences.
delta.glm: no visible global function definition for 'glm'
delta.glm: no visible global function definition for 'residuals'
delta.glm: no visible global function definition for 'fitted'
delta.glm: no visible global function definition for 'predict.glm'
two.stage.model.outputs: no visible global function definition for 'sd'
Undefined global functions or variables:
  fitted glm predict.glm residuals sd
Consider adding
  importFrom("stats", "fitted", "glm", "predict.glm", "residuals", "sd")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/CVarE/CVarE.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
ci.cvAUC: no visible global function definition for 'qnorm'
ci.pooled.cvAUC: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  qnorm
Consider adding
  importFrom("stats", "qnorm")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Malformed Description field: should contain one or more complete sentences.
calfun: no visible global function definition for 'optim'
calfun: no visible global function definition for 'cov'
calfun: no visible global function definition for 'var'
Undefined global functions or variables:
  cov optim var
Consider adding
  importFrom("stats", "cov", "optim", "var")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'spelling'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'MBESS'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages which this enhances but not available for checking: 'png', 'RGtk2'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'pkgdown'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
func.constructRegressionFormula: no visible global function definition
  for 'as.formula'
func.crossValidationAnalysis: no visible global function definition for
  'glm'
func.crossValidationAnalysis: no visible global function definition for
  'predict'
func.crossValidationAnalysis: no visible global function definition for
  'write.table'
func.externalValidationAnalysis: no visible global function definition
  for 'predict'
func.externalValidationAnalysis: no visible global function definition
  for 'write.table'
func.linearRegressionAnalysis: no visible global function definition
  for 'glm'
func.linearRegressionAnalysis: no visible global function definition
  for 'predict'
func.linearRegressionAnalysis: no visible global function definition
  for 'write.table'
func.sortDataColumns: no visible global function definition for
  'write.table'
mainfunc.q2: no visible global function definition for 'write.table'
mainfunc.q2: no visible global function definition for 'new'
mainfunc.stats: no visible global function definition for 'write.table'
mainfunc.stats: no visible global function definition for 'new'
Undefined global functions or variables:
  as.formula glm new predict write.table
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "as.formula", "glm", "predict")
  importFrom("utils", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/CVR/CVR.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
cvimpute.by.wavelet: no visible global function definition for 'sd'
cvimpute.by.wavelet: no visible global function definition for 'mad'
cvimpute.image.by.wavelet: no visible global function definition for
  'sd'
cvimpute.image.by.wavelet: no visible global function definition for
  'mad'
cvwavelet.image.after.impute: no visible global function definition for
  'sd'
cvwavelet.image.after.impute: no visible global function definition for
  'mad'
Undefined global functions or variables:
  mad sd
Consider adding
  importFrom("stats", "mad", "sd")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'lattice' 'robustbase'
A package should be listed in only one of these fields.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
random.CV: no visible global function definition for 'var'
regular.CV: no visible global function definition for 'var'
Undefined global functions or variables:
  var
Consider adding
  importFrom("stats", "var")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages which this enhances but not available for checking:
  'Rcplex', 'gurobi', 'rcbc'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/CVXR/CVXR.Rcheck/00install.out' for details.
Packages required but not available: 'xml2', 'RcppCWB', 'zen4R'

Packages suggested but not available for checking: 'tm', 'aws.s3'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
.mixgauss_init: no visible global function definition for 'cov'
.mixgauss_init: no visible global function definition for 'var'
Undefined global functions or variables:
  cov var
Consider adding
  importFrom("stats", "cov", "var")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/cxhull/cxhull.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'hydroPSO'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
cxxfun.from.dll: no visible global function definition for 'new'
cxxfun.from.dso.bin: no visible global function definition for 'new'
cxxfunctionplus: no visible global function definition for 'getPlugin'
cxxfunctionplus: no visible global function definition for
  'cxxfunction'
cxxfunctionplus: no visible global function definition for 'new'
show,cxxdso: no visible global function definition for 'object.size'
Undefined global functions or variables:
  cxxfunction getPlugin new object.size
Consider adding
  importFrom("methods", "new")
  importFrom("utils", "object.size")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'xml2'

Package suggested but not available for checking: 'leaflet'

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

Package suggested but not available for checking: 'stplanr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/Cyclops/Cyclops.Rcheck/00install.out' for details.
Package required but not available: 'rgl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package in Depends field not imported from: 'fda'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
check.for.sequence.endpoint.breaks: no visible global function
  definition for 'na.omit'
get.breaks.vector: no visible global function definition for 'na.omit'
get.cycle.breaks: no visible global function definition for 'na.omit'
get.cycle.counts: no visible global function definition for 'na.omit'
get.cycle.matrix: no visible global function definition for 'na.omit'
get.cycle.minimums: no visible global function definition for 'na.omit'
get.peaks: no visible global function definition for 'embed'
get.trans: no visible global function definition for
  'create.bspline.basis'
get.trans: no visible global function definition for 'smooth.basis'
get.trans: no visible global function definition for 'deriv.fd'
get.trans: no visible global function definition for 'eval.fd'
get.transition.locations: no visible global function definition for
  'na.omit'
get.transition.locations.FDiff: no visible global function definition
  for 'na.omit'
get.window: no visible global function definition for 'sd'
Undefined global functions or variables:
  create.bspline.basis deriv.fd embed eval.fd na.omit sd smooth.basis
Consider adding
  importFrom("stats", "embed", "na.omit", "sd")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Malformed Description field: should contain one or more complete sentences.
cytoDiv: no visible global function definition for 'colorRampPalette'
cytoDiv: no visible global function definition for 'persp'
Undefined global functions or variables:
  colorRampPalette persp
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "persp")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'titanic'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages which this enhances but not available for checking:
  'igraph', 'treemap'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'magrittr'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'DAAG'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'latticeExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'vdiffr'
Namespaces in Imports field not imported from:
  'plyr' 'simpleboot'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'png'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Note: found 4 marked Latin-1 strings
  Note: found 21 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'FrF2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: 's20x'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'knitr'
  All declared Imports should be used.
Note: found 212 marked Latin-1 strings
  Note: found 12719 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespaces in Imports field not imported from:
  'curl' 'fs' 'googleCloudStorageR'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'DDD'

Package suggested but not available for checking: 'phytools'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'reticulate'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/DALY/DALY.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'rstan', 'latticeExtra'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'lintr', 'kableExtra'
Error(s) in re-building vignettes:
--- re-building 'basic_cea.Rmd' using rmarkdown
Quitting from lines 81-86 (basic_cea.Rmd) 
Error: processing vignette 'basic_cea.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'basic_cea.Rmd'

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

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

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

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

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

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Note: found 5 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dang/dang.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dann/dann.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'kableExtra'
'LazyData' is specified without a 'data' directory
Running examples in 'danstat-Ex.R' failed
The error most likely occurred in:

> ### Name: get_subjects
> ### Title: Get a list of subjects covered in the data bank
> ### Aliases: get_subjects
> 
> ### ** Examples
> 
> # Get all subjects
> all_subjects <- get_subjects()
> 
> # Or get (sub)subjects for specific subjects
> some_subjects <- get_subjects(subjects = c("02", "2419"))
Error: API did not return text/json
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(danstat)
  > 
  > test_check("danstat")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-get_tables.R:2:3): subject 'as is' I() works ────────────────────
  Error: API did not return text/json
  Backtrace:
      █
   1. ├─testthat::expect_identical(get_tables(subjects = "2419"), get_tables(subjects = c("2419"))) test-get_tables.R:2:2
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─danstat::get_tables(subjects = "2419")
   5.   └─danstat:::check_http_type(result)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 18 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'Introduction_to_danstat.Rmd' using rmarkdown
Quitting from lines 24-29 (Introduction_to_danstat.Rmd) 
Error: processing vignette 'Introduction_to_danstat.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'Introduction_to_danstat.Rmd'

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

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/DAP/DAP.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'xesreadR'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available:
  'adegenet', 'StAMPP', 'PopGenReport', 'hierfstat', 'devtools'

Packages suggested but not available for checking:
  'rgl', 'pca3d', 'pegas', 'rgdal', 'leaflet.minicharts', 'leaflet',
  'poppr', 'igraph', 'gdistance', 'mmod'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/darts/darts.Rcheck/00install.out' for details.
dashboard_open: no visible global function definition for 'write.csv'
dashboard_open: no visible global function definition for
  'capture.output'
dctable: no visible global function definition for 'capture.output'
Undefined global functions or variables:
  capture.output write.csv
Consider adding
  importFrom("utils", "capture.output", "write.csv")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'lintr'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'dash'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'dash'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'dash'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'fiery', 'routr', 'reqres'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'dash'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/Data2LD/Data2LD.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'curl'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'aws.s3'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking:
  'spdep', 'rgl', 'png', 'parallelDist'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/DatabionicSwarm/DatabionicSwarm.Rcheck/00install.out' for details.
Package required but not available: 'XML'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'devtools'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'RGtk2', 'gWidgets2RGtk2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'networkD3'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/datafsm/datafsm.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/DataGraph/DataGraph.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/datamap/datamap.Rcheck/00install.out' for details.
Package required but not available: 'XML'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'XML', 'datapack'

Package suggested but not available for checking: 'xml2'

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

Package suggested but not available for checking: 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'roxygen2', 'devtools'

Package suggested but not available for checking: 'spelling'

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

Package suggested but not available for checking: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'vdiffr'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'xml2'

Package suggested but not available for checking: 'sf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'lintr'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/datasailr/datasailr.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'EML'

Package suggested but not available for checking: 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/DatAssim/DatAssim.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Note: found 8 marked Latin-1 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'lintr'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/datastructures/datastructures.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/data.table/data.table.Rcheck/00install.out' for details.
Packages suggested but not available for checking:
  'networkD3', 'treemap', 'DiagrammeR'

Package which this enhances but not available for checking: 'igraph'
Package unavailable to check Rd xrefs: 'DiagrammeR'
Running examples in 'data.tree-Ex.R' failed
The error most likely occurred in:

> ### Name: plot.Node
> ### Title: Plot a graph, or get a graphviz dot representation of the tree
> ### Aliases: plot.Node ToDiagrammeRGraph SetNodeStyle SetEdgeStyle
> ###   SetGraphStyle GetDefaultTooltip
> 
> ### ** Examples
> 
> data(acme)
> SetGraphStyle(acme, rankdir = "TB")
> SetEdgeStyle(acme, arrowhead = "vee", color = "blue", penwidth = 2)
> #per default, Node style attributes will be inherited:
> SetNodeStyle(acme, style = "filled,rounded", shape = "box", fillcolor = "GreenYellow", 
+              fontname = "helvetica", tooltip = GetDefaultTooltip)
> SetNodeStyle(acme$IT, fillcolor = "LightBlue", penwidth = "5px")
> #inheritance can be avoided:
> SetNodeStyle(acme$Accounting, inherit = FALSE, fillcolor = "Thistle", 
+              fontcolor = "Firebrick", tooltip = "This is the accounting department")
> SetEdgeStyle(acme$Research$`New Labs`, 
+              color = "red", 
+              label = "Focus!", 
+              penwidth = 3, 
+              fontcolor = "red")
> #use Do to set style on specific nodes:
> Do(acme$leaves, function(node) SetNodeStyle(node, shape = "egg"))
> plot(acme)
Error in plot.Node(acme) : 
  Package "DiagrammeR" is required to plot a `data.tree::Node`object. Please install it.
Calls: plot -> plot.Node
Execution halted
Error(s) in re-building vignettes:
--- re-building 'applications.Rmd' using rmarkdown
Quitting from lines 57-64 (applications.Rmd) 
Error: processing vignette 'applications.Rmd' failed with diagnostics:
there is no package called 'treemap'
--- failed re-building 'applications.Rmd'

--- re-building 'data.tree.Rmd' using rmarkdown
Quitting from lines 121-124 (data.tree.Rmd) 
Error: processing vignette 'data.tree.Rmd' failed with diagnostics:
there is no package called 'treemap'
--- failed re-building 'data.tree.Rmd'

SUMMARY: processing the following files failed:
  'applications.Rmd' 'data.tree.Rmd'

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespaces in Imports field not imported from:
  'R6' 'rmarkdown' 'shiny'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'xml2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'ggmap', 'rgl', 'choroplethr', 'parallelDist'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/DataVisualizations/DataVisualizations.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/DataViz/DataViz.Rcheck/00install.out' for details.
Packages suggested but not available for checking: 'rstanarm', 'spelling'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available:
  'sidrar', 'geobr', 'sf', 'XML', 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/date/date.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'SASxport'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Note: found 54313 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'devtools'
Note: found 1 marked Latin-1 string
  Note: found 360 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'aoos'

Package suggested but not available for checking: 'lintr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dauphin/dauphin.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'sf'

Package suggested but not available for checking: 'rgdal'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dbarts/dbarts.Rcheck/00install.out' for details.
Packages required but not available: 'TSdist', 'parallelDist'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Malformed Description field: should contain one or more complete sentences.
dbEmpLikeGOF: no visible global function definition for 'runif'
dbEmpLikeGOF: no visible global function definition for 'var'
dbEmpLikeGOF: no visible global function definition for 'rnorm'
emplikeGOFinternal: no visible global function definition for 'var'
getCutoff: no visible binding for global variable 'unifCut'
getCutoff: no visible binding for global variable 'normCut'
getCutoff: no visible global function definition for 'lm'
getCutoff: no visible binding for global variable 'distEqCut'
getPval: no visible binding for global variable 'unifCut'
getPval: no visible binding for global variable 'normCut'
getPval: no visible global function definition for 'lm'
getPval: no visible binding for global variable 'distEqCut'
helperPval: no visible global function definition for 'lm'
returnCutoff: no visible global function definition for 'quantile'
testfun2: no visible global function definition for 'runif'
testfun2: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  distEqCut lm normCut quantile rnorm runif unifCut var
Consider adding
  importFrom("stats", "lm", "quantile", "rnorm", "runif", "var")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Malformed Description field: should contain one or more complete sentences.
computePval: no visible global function definition for 'lm'
computeQhat: no visible global function definition for 'pnorm'
dbELnorm: no visible global function definition for 'rnorm'
getCutoffTableThree: no visible global function definition for 'lm'
getCutoffTableTwo: no visible global function definition for 'lm'
getCutoffValue: no visible global function definition for 'lm'
helperGetTstat: no visible global function definition for 'rnorm'
returnCutoffValue: no visible global function definition for 'rnorm'
returnCutoffValue: no visible global function definition for 'quantile'
varianceEstimator: no visible global function definition for 'density'
varianceEstimator: no visible global function definition for 'ecdf'
Undefined global functions or variables:
  density ecdf lm pnorm quantile rnorm
Consider adding
  importFrom("stats", "density", "ecdf", "lm", "pnorm", "quantile",
             "rnorm")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Title field: should not end in a period.
'library' or 'require' call to 'fdrtool' which was already attached by Depends.
  Please remove these calls from your code.
avelinkdis: no visible global function definition for 'sd'
avelinkdis: no visible global function definition for 'dist'
centdis: no visible global function definition for 'sd'
centdis: no visible global function definition for 'dist'
distable: no visible global function definition for 'write.table'
functionall: no visible global function definition for 'read.table'
randdis: no visible global function definition for 'write.table'
valuep: no visible global function definition for 'write.csv'
Undefined global functions or variables:
  dist read.table sd write.csv write.table
Consider adding
  importFrom("stats", "dist", "sd")
  importFrom("utils", "read.table", "write.csv", "write.table")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'XML'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'xml2'
Error(s) in re-building vignettes:
--- re-building 'DBI-1.Rmd' using rmarkdown
--- finished re-building 'DBI-1.Rmd'

--- re-building 'DBI-advanced.Rmd' using rmarkdown
--- finished re-building 'DBI-advanced.Rmd'

--- re-building 'DBI-history.Rmd' using rmarkdown
--- finished re-building 'DBI-history.Rmd'

--- re-building 'DBI-proposal.Rmd' using rmarkdown
--- finished re-building 'DBI-proposal.Rmd'

--- re-building 'DBI.Rmd' using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

--- finished re-building 'DBI.Rmd'

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

--- re-building 'spec.Rmd' using rmarkdown
Quitting from lines 27-31 (spec.Rmd) 
Error: processing vignette 'spec.Rmd' failed with diagnostics:
there is no package called 'xml2'
--- failed re-building 'spec.Rmd'

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

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking:
  'dblog', 'devtools', 'lintr'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dblcens/dblcens.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dBlockmodeling/dBlockmodeling.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'softImpute'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'RcppParallel'

Package suggested but not available for checking: 'pkgdown'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dbnR/dbnR.Rcheck/00install.out' for details.
Package required but not available: 'XML'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'igraph'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dbscan/dbscan.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'html5'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'c3net', 'igraph', 'RedeR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/DCCA/DCCA.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'Ecdat'
Package unavailable to check Rd xrefs: 'Ecdat'
Running examples in 'DCchoice-Ex.R' failed
The error most likely occurred in:

> ### Name: dbchoice
> ### Title: Parametric approach to analyze double-bounded dichotomous choice
> ###   contingent valuation data
> ### Aliases: dbchoice print.dbchoice vcov.dbchoice logLik.dbchoice
> ### Keywords: DCchoice double-bounded nonlinear
> 
> ### ** Examples
> 
> ## Examples are based on a data set NaturalPark in the package 
> ## Ecdat (Croissant 2011): DBDCCV style question for measuring 
> ## willingness to pay for the preservation of the Alentejo Natural 
> ## Park. The data set (dataframe) contains seven variables: 
> ## bid1 (bid in the initial question), bidh (higher bid in the follow-up 
> ## question), bidl (lower bid in the follow-up question), answers 
> ## (response outcomes in a factor format with four levels of "nn", 
> ## "ny", "yn", "yy"), respondents' characteristic variables such 
> ## as age, sex and income (see NaturalPark for details).
> data(NaturalPark, package = "Ecdat")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called 'Ecdat'
Calls: data -> find.package
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'rumidas', 'roll'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/DCEM/DCEM.Rcheck/00install.out' for details.
Namespaces in Imports field not imported from:
  'commonmark' 'htmltools' 'readxl'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

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

Package suggested but not available for checking: 'doMC'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'devtools', 'png'
Error(s) in re-building vignettes:
--- re-building 'Introduction_to_DCG.Rmd' using rmarkdown
Quitting from lines 59-61 (Introduction_to_DCG.Rmd) 
Error: processing vignette 'Introduction_to_DCG.Rmd' failed with diagnostics:
there is no package called 'png'
--- failed re-building 'Introduction_to_DCG.Rmd'

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

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'phangorn', 'igraph', 'tidyverse'

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

Package suggested but not available for checking: 'BRugs'

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.
Package required but not available: 'DCluster'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'CDM'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'dclone'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dcov/dcov.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'rstan', 'rstantools', 'StanHeaders'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/DCSmooth/DCSmooth.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dcurver/dcurver.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'spelling'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
test.LM: no visible global function definition for 'lm'
Undefined global functions or variables:
  lm
Consider adding
  importFrom("stats", "lm")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ddalpha/ddalpha.Rcheck/00install.out' for details.
Package required but not available: 'phytools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dde/dde.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/DDHFm/DDHFm.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespaces in Imports field not imported from:
  'MASS' 'qpdf'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'xml2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'MEGENA', 'igraph', 'Hmisc'

Package suggested but not available for checking: 'WGCNA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/DDRTree/DDRTree.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/deal/deal.Rcheck/00install.out' for details.
ifft: no visible global function definition for 'fft'
lines.deamer: no visible global function definition for 'lines'
rlaplace: no visible global function definition for 'runif'
Undefined global functions or variables:
  fft lines runif
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "fft", "runif")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'devtools'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/DeCAFS/DeCAFS.Rcheck/00install.out' for details.
compare.relimp: no visible global function definition for 'qchisq'
compare.relimp: no visible global function definition for 'pchisq'
plot_transition: no visible global function definition for 'dnorm'
plot_transition: no visible global function definition for 'par'
plot_transition: no visible global function definition for 'lines'
plot_transition: no visible global function definition for 'plogis'
plot_transition: no visible global function definition for 'axis'
plot_transition: no visible global function definition for 'mtext'
relative.importance: no visible global function definition for 'glm'
relative.importance: no visible global function definition for 'sd'
relative.importance : tr.pr: no visible global function definition for
  'pnorm'
relative.importance: no visible global function definition for 'vcov'
Undefined global functions or variables:
  axis dnorm glm lines mtext par pchisq plogis pnorm qchisq sd vcov
Consider adding
  importFrom("graphics", "axis", "lines", "mtext", "par")
  importFrom("stats", "dnorm", "glm", "pchisq", "plogis", "pnorm",
             "qchisq", "sd", "vcov")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'spelling'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/decido/decido.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'chillR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'sf'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'sf'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Note: found 1 marked Latin-1 string
  Note: found 46826 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'StratigrapheR'

Package suggested but not available for checking: 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/decompr/decompr.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/decon/decon.Rcheck/00install.out' for details.
Packages required but not available:
  'BSgenome', 'BSgenome.Hsapiens.UCSC.hg19'

Package suggested but not available for checking: 'VariantAnnotation'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/decor/decor.Rcheck/00install.out' for details.
Package in Depends field not imported from: 'Deducer'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Depends: includes the non-default packages:
  'Deducer', 'psych', 'GPArotation', 'mvnormtest', 'irr', 'klaR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'library' or 'require' call to 'klaR' which was already attached by Depends.
  Please remove these calls from your code.
.makeICCDialog: no visible global function definition for 'J'
.makeICCDialog: no visible global function definition for 'new'
.makeICCDialog: no visible global function definition for '.jnull'
.makeNewFactorAnalysisDialog: no visible global function definition for
  'new'
.makeNewFactorAnalysisDialog: no visible global function definition for
  'J'
.makeNewFactorAnalysisDialog: no visible global function definition for
  'toJava'
.makeNewLDADialog: no visible global function definition for 'new'
.makeNewLDADialog: no visible global function definition for 'J'
.makeNewLDADialog : linkSubDialog: no visible global function
  definition for 'new'
.makeNewLDADialog : linkSubDialog: no visible global function
  definition for 'toJava'
.makeNewLDADialog: no visible global function definition for 'toJava'
.makeNewReliabilityDialog: no visible global function definition for
  'new'
.makeNewReliabilityDialog: no visible global function definition for
  'toJava'
.onLoad: no visible global function definition for '.jnull'
.onLoad: no visible global function definition for 'winMenuAdd'
.onLoad: no visible global function definition for 'winMenuAddItem'
.onLoad: no visible global function definition for 'jgr.getMenuNames'
.onLoad: no visible global function definition for 'jgr.insertMenu'
.onLoad: no visible global function definition for 'jgr.addMenu'
.onLoad: no visible global function definition for 'jgr.addMenuItem'
Undefined global functions or variables:
  .jnull J jgr.addMenu jgr.addMenuItem jgr.getMenuNames jgr.insertMenu
  new toJava winMenuAdd winMenuAddItem
Consider adding
  importFrom("methods", "new")
  importFrom("utils", "winMenuAdd", "winMenuAddItem")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'Hmisc'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'OpenStreetMap', 'rgdal', 'Hmisc'

Depends: includes the non-default packages:
  'JavaGD', 'Deducer', 'sp', 'maptools', 'OpenStreetMap', 'scales',
  'rgdal'
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: 'Deducer'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'tm'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/deductive/deductive.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'kableExtra'
Error(s) in re-building vignettes:
--- re-building 'usage-and-algorithm-explained.Rmd' using rmarkdown
Quitting from lines 19-23 (usage-and-algorithm-explained.Rmd) 
Error: processing vignette 'usage-and-algorithm-explained.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'usage-and-algorithm-explained.Rmd'

SUMMARY: processing the following file failed:
  'usage-and-algorithm-explained.Rmd'

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/deepboost/deepboost.Rcheck/00install.out' for details.
Packages required but not available: 'ggraph', 'graphlayouts', 'igraph'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/deepgp/deepgp.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'dplyr'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
binary.state: no visible global function definition for 'runif'
dbn.dnn.train: no visible global function definition for 'runif'
dropout.mask: no visible global function definition for 'runif'
nn.train: no visible global function definition for 'runif'
rbm.train: no visible global function definition for 'runif'
sae.dnn.train: no visible global function definition for 'runif'
show.digit: no visible global function definition for 'gray'
show.digit: no visible global function definition for 'image'
Undefined global functions or variables:
  gray image runif
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "image")
  importFrom("stats", "runif")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'keras', 'reticulate', 'tensorflow'

Package suggested but not available for checking: 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
DEEPR : perm_function: no visible global function definition for 'head'
DEEPR : perm_function: no visible global function definition for 'tail'
simCophy: no visible global function definition for 'rpois'
simCophy: no visible global function definition for 'rmultinom'
Undefined global functions or variables:
  head rmultinom rpois tail
Consider adding
  importFrom("stats", "rmultinom", "rpois")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking:
  'tidyverse', 'phytools', 'paleotree', 'dispRity', 'vdiffr'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(deeptime)
  > 
  > test_check("deeptime")
  Error in library(tidyverse, quietly = TRUE) : 
    there is no package called 'tidyverse'
  Calls: test_check ... suppressPackageStartupMessages -> withCallingHandlers -> library
  Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'Hmisc', 'SASxport'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/deformula/deformula.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/Delaporte/Delaporte.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/deldir/deldir.Rcheck/00install.out' for details.
Packages required but not available: 'rstan', 'rstantools', 'StanHeaders'

Package suggested but not available for checking: 'knitcitations'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/delt/delt.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'knitr'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'officer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/demu/demu.Rcheck/00install.out' for details.
Package which this enhances but not available for checking: 'Hmisc'
Packages unavailable to check Rd xrefs: 'WGCNA', 'phangorn'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'oce'

Package suggested but not available for checking: 'dplR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/DendSer/DendSer.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/denpro/denpro.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'mvtnorm'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'rstan', 'RcppParallel', 'StanHeaders'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/densityClust/densityClust.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'devtools', 'roxygen2'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/DEoptim/DEoptim.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/depcoeff/depcoeff.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'Hmisc', 'rms'

Package suggested but not available for checking: 'spelling'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'Rdonlp2'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/depmix/depmix.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'Rdonlp2'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/depmixS4/depmixS4.Rcheck/00install.out' for details.
Packages required but not available: 'xml2', 'rgdal'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'rgl', 'lintr'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/DepthProc/DepthProc.Rcheck/00install.out' for details.
Package required but not available: 'rgl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dequer/dequer.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'spelling'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'roxygen2'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'lintr'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Note: found 5764 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'vdiffr'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/descr/descr.Rcheck/00install.out' for details.
Packages required but not available: 'kableExtra', 'flextable', 'officer'

Package suggested but not available for checking: 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'datasets'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'RDCOMClient'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/DescTools/DescTools.Rcheck/00install.out' for details.
ds: no visible global function definition for 'is.ts'
ds: no visible global function definition for 'frequency'
getds: no visible global function definition for 'resid'
getds: no visible global function definition for 'lm.fit'
getds: no visible global function definition for 'sd'
getds: no visible global function definition for 'var'
getds: no visible global function definition for 'fitted'
Undefined global functions or variables:
  fitted frequency is.ts lm.fit resid sd var
Consider adding
  importFrom("stats", "fitted", "frequency", "is.ts", "lm.fit", "resid",
             "sd", "var")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'reticulate'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Title field: should not end in a period.
arrayUpdate : pairUpdate: no visible global function definition for
  'runif'
conditionUpdate: no visible global function definition for 'runif'
designGG: no visible global function definition for 'runif'
experimentDesignTable: no visible global function definition for
  'write.csv'
plotAllScores: no visible global function definition for 'png'
plotAllScores: no visible global function definition for 'par'
plotAllScores: no visible global function definition for 'text'
plotAllScores: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  dev.off par png runif text write.csv
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "par", "text")
  importFrom("stats", "runif")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Note: found 47 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/desire/desire.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
fs.agreement.part: no visible global function definition for 'as.dist'
fs.agreement.part: no visible global function definition for 'cor'
fs.leave.k.out.combn: no visible global function definition for 'sd'
fs.leave.k.out.sample: no visible global function definition for 'sd'
fs.rd: no visible global function definition for 'pchisq'
fs.selection: no visible global function definition for 'p.adjust'
plot.FIT: no visible global function definition for 'qchisq'
plot.FIT: no visible global function definition for 'ppoints'
plot.FIT: no visible global function definition for 'points'
plot.FIT: no visible global function definition for 'abline'
plotJn: no visible global function definition for 'points'
robust.distance.signed: no visible global function definition for
  'mahalanobis'
snowball: no visible global function definition for 'is'
snowball: no visible global function definition for 'median'
weight.sd: no visible binding for global variable 'sd'
Undefined global functions or variables:
  abline as.dist cor is mahalanobis median p.adjust pchisq points
  ppoints qchisq sd
Consider adding
  importFrom("graphics", "abline", "points")
  importFrom("methods", "is")
  importFrom("stats", "as.dist", "cor", "mahalanobis", "median",
             "p.adjust", "pchisq", "ppoints", "qchisq", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/deSolve/deSolve.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'png', 'xml2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'dclone', 'dcmle'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/detectRUNS/detectRUNS.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'ROI.plugin.neos'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/deTestSet/deTestSet.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/DetMCD/DetMCD.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'dplR'

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

Package suggested but not available for checking: 'spelling'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/DetR/DetR.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/DetSel/DetSel.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'RColorBrewer'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespaces in Imports field not imported from:
  'DT' 'utils'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/devEMF/devEMF.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/devoid/devoid.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespaces in Imports field not imported from:
  'DT' 'ggiraph' 'ggplot2' 'reshape2' 'stats' 'tidyr' 'tidyselect'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'roxygen2', 'rversions'

Packages suggested but not available for checking:
  'foghorn', 'lintr', 'pkgdown', 'spelling'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'readODS', 'networkD3', 'Cairo'

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

Package suggested but not available for checking: 'Cairo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'latticeExtra', 'Cairo'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dexter/dexter.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'spelling'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dfcomb/dfcomb.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
simulate_dataframe : generate_dumb_answer: no visible global function
  definition for 'rbinom'
simulate_dataframe : generate_dumb_answer: no visible global function
  definition for 'rnorm'
simulate_dataframe : generate_initial: no visible global function
  definition for 'rbinom'
simulate_dataframe: no visible binding for global variable 'randu'
simulate_dataframe: no visible global function definition for 'rbinom'
simulate_dataframe: no visible global function definition for 'rnorm'
simulate_dataframe: no visible global function definition for 'rpois'
simulate_dataframe : add_NAs: no visible global function definition for
  'rbinom'
Undefined global functions or variables:
  randu rbinom rnorm rpois
Consider adding
  importFrom("datasets", "randu")
  importFrom("stats", "rbinom", "rnorm", "rpois")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dfmta/dfmta.Rcheck/00install.out' for details.
Package required but not available: 'dplR'

Package suggested but not available for checking: 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Note: found 1 marked UTF-8 string
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'rstan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dfphase1/dfphase1.Rcheck/00install.out' for details.
Packages required but not available: 'rstan', 'StanHeaders'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dga/dga.Rcheck/00install.out' for details.
Packages required but not available: 'MLInterfaces', 'genefilter'

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

Packages suggested but not available for checking:
  'GOstats', 'org.Hs.eg.db', 'AnnotationDbi', 'MEGENA', 'doMC',
  'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'biomaRt'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'sva'

Package suggested but not available for checking: 'biomaRt'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dglars/dglars.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/DGM/DGM.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dgof/dgof.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dgumbel/dgumbel.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'phyr'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dHSIC/dHSIC.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'rlang'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/diagis/diagis.Rcheck/00install.out' for details.
Package required but not available: 'meta'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'igraph', 'influenceR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'reticulate', 'sf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'xml2'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Note: found 7880 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'rgl'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/DiceDesign/DiceDesign.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/DiceKriging/DiceKriging.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'GPareto'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/DiceOptim/DiceOptim.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/diceR/diceR.Rcheck/00install.out' for details.
Package which this enhances but not available for checking: 'rgl'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
dichromat: no visible global function definition for 'col2rgb'
dichromat: no visible global function definition for 'predict'
dichromat: no visible global function definition for 'rgb'
Undefined global functions or variables:
  col2rgb predict rgb
Consider adding
  importFrom("grDevices", "col2rgb", "rgb")
  importFrom("stats", "predict")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
le.pesquisa: no visible global function definition for 'txtProgressBar'
le.pesquisa: no visible global function definition for 'type.convert'
le.pesquisa: no visible global function definition for
  'setTxtProgressBar'
Undefined global functions or variables:
  setTxtProgressBar txtProgressBar type.convert
Consider adding
  importFrom("utils", "setTxtProgressBar", "txtProgressBar",
             "type.convert")
to your NAMESPACE file.
Note: found 2297 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespaces in Imports field not imported from:
  'R6' 'dplyr' 'purrr'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/didimputation/didimputation.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'knitr'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Malformed Title field: should not end in a period.
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
L2eV: no visible binding for global variable 'constants'
L2w: no visible binding for global variable 'constants'
dielectric: no visible global function definition for 'new'
dielectric2plot: no visible global function definition for 'reshape'
eV2L: no visible binding for global variable 'constants'
t2eV: no visible binding for global variable 'constants'
Undefined global functions or variables:
  constants new reshape
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "reshape")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages in Depends field not imported from:
  'PropCIs' 'gee' 'rootSolve'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
diffpci: no visible global function definition for 'diffpropci.Wald.mp'
diffpci: no visible global function definition for 'diffpropci.mp'
diffpci: no visible global function definition for 'scoreci.mp'
exact.cond : exactci: no visible global function definition for 'qf'
exact.midp : binom.midp : f.low: no visible global function definition
  for 'dbinom'
exact.midp : binom.midp : f.low: no visible global function definition
  for 'pbinom'
exact.midp : binom.midp : f.up: no visible global function definition
  for 'dbinom'
exact.midp : binom.midp : f.up: no visible global function definition
  for 'pbinom'
exact.midp : binom.midp : one.ci: no visible global function definition
  for 'uniroot'
np.nv: no visible global function definition for 'qnorm'
np.t: no visible global function definition for 'qt'
uncond: no visible global function definition for 'qnorm'
wald.cc: no visible global function definition for 'qnorm'
wilson: no visible global function definition for 'qnorm'
wilson: no visible global function definition for 'uniroot.all'
wilson.cc: no visible global function definition for 'qnorm'
wilson.cc: no visible global function definition for 'uniroot.all'
wilson.phi: no visible global function definition for 'qnorm'
wilson.phi: no visible global function definition for 'uniroot.all'
Undefined global functions or variables:
  dbinom diffpropci.Wald.mp diffpropci.mp pbinom qf qnorm qt scoreci.mp
  uniroot uniroot.all
Consider adding
  importFrom("stats", "dbinom", "pbinom", "qf", "qnorm", "qt", "uniroot")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'devtools'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'kableExtra'
Error(s) in re-building vignettes:
--- re-building 'diffenrich_vignette.Rmd' using rmarkdown
Loading required package: kableExtra
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'kableExtra'
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'kableExtra'
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'kableExtra'
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'kableExtra'
Quitting from lines 339-342 (diffenrich_vignette.Rmd) 
Error: processing vignette 'diffenrich_vignette.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'diffenrich_vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'rgdal'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/diffIRT/diffIRT.Rcheck/00install.out' for details.
Packages required but not available: 'tidyverse', 'igraph', 'sf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/diffmatchpatch/diffmatchpatch.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'Hmisc', 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/diffobj/diffobj.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'rgl'

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

Packages suggested but not available for checking:
  'DiffusionRgqd', 'DiffusionRjgqd'

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

Package suggested but not available for checking: 'DiffusionRgqd'

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

Package suggested but not available for checking: 'lintr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'ShinyItemAnalysis'
Running examples in 'difNLR-Ex.R' failed
The error most likely occurred in:

> ### Name: difORD
> ### Title: DIF detection among ordinal data.
> ### Aliases: difORD
> ### Keywords: DIF
> 
> ### ** Examples
> 
> # Loading data
> data(dataMedicalgraded, package = "ShinyItemAnalysis")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called 'ShinyItemAnalysis'
Calls: data -> find.package
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/digest/digest.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'readbitmap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'bibliometrix'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'vdiffr'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/DIME/DIME.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking:
  'cccd', 'diffusionMap', 'igraph', 'keras', 'pcaL1', 'reticulate',
  'rgl', 'tensorflow', 'umap'
Packages unavailable to check Rd xrefs: 'keras', 'diffusionMap', 'igraph', 'umap', 'reticulate'
'LazyData' is specified without a 'data' directory
Running examples in 'dimRed-Ex.R' failed
The error most likely occurred in:

> ### Name: DiffusionMaps-class
> ### Title: Diffusion Maps
> ### Aliases: DiffusionMaps-class DiffusionMaps
> 
> ### ** Examples
> 
> dat <- loadDataSet("3D S Curve", n = 300)
> 
> ## use the S4 Class directly:
> diffmap <- DiffusionMaps()
> emb <- diffmap@fun(dat, diffmap@stdpars)
Error in chckpkg("diffusionMap") : 
  require 'diffusionMap' package, install it using install.packages('diffusionMap')
Calls: <Anonymous> -> chckpkg
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dina/dina.Rcheck/00install.out' for details.
Package required but not available: 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'WGCNA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dipm/dipm.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'RcppParallel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/diptest/diptest.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'sandwich'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'rgl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'latticeExtra'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/DIRECT/DIRECT.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/Dire/Dire.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'rgl'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/DirichletReg/DirichletReg.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Malformed Title field: should not end in a period.
nullTest: no visible global function definition for 'rmultinom'
rdirichlet: no visible global function definition for 'rgamma'
simPop: no visible global function definition for 'rnorm'
simPop: no visible global function definition for 'rmultinom'
Undefined global functions or variables:
  rgamma rmultinom rnorm
Consider adding
  importFrom("stats", "rgamma", "rmultinom", "rnorm")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/DirStats/DirStats.Rcheck/00install.out' for details.
Package required but not available: 'rgdal'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'shinytest', 'vdiffr'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available:
  'TSCAN', 'igraph', 'png', 'AnnotationDbi', 'org.Hs.eg.db'

Package suggested but not available for checking: 'Seurat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'xml2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/disclapmix/disclapmix.Rcheck/00install.out' for details.
Malformed Description field: should contain one or more complete sentences.
rdisclap: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'psych'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'tmod'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

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 required but not available: 'golem'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/DiscreteFDR/DiscreteFDR.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
p.discrete.adjust : <anonymous>: no visible global function definition
  for 'stepfun'
Undefined global functions or variables:
  stepfun
Consider adding
  importFrom("stats", "stepfun")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'roxygen2'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Malformed Title field: should not end in a period.
value: no visible global function definition for 'qchisq'
Undefined global functions or variables:
  qchisq
Consider adding
  importFrom("stats", "qchisq")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Malformed Description field: should contain one or more complete sentences.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'spelling', 'xml2'
Namespace in Imports field not imported from: 'utils'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'Ecdat', 'pec'
Running examples in 'discSurv-Ex.R' failed
The error most likely occurred in:

> ### Name: adjDevResid
> ### Title: Adjusted Deviance Residuals
> ### Aliases: adjDevResid
> ### Keywords: survival
> 
> ### ** Examples
> 
> # Example with cross validation and unemployment data 
> library(Ecdat)
Error in library(Ecdat) : there is no package called 'Ecdat'
Execution halted
Running 'UnitTestsDiscSurvDataTransform.R'
  Running 'UnitTestsDiscSurvEstimation.R'
  Running 'UnitTestsDiscSurvEvalShort.R'
  Running 'UnitTestsDiscSurvEvaluation.R'
Running the tests in 'tests/UnitTestsDiscSurvEvaluation.R' failed.
Complete output:
  > library(discSurv)
  > library(pec)
  Error in library(pec) : there is no package called 'pec'
  Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking:
  'sf', 'terra', 'rgdal', 'mapview'
Running examples in 'disdat-Ex.R' failed
The error most likely occurred in:

> ### Name: AWT
> ### Title: Australian Wet Tropics species distribution data
> ### Aliases: AWT
> ### Keywords: datasets
> 
> ### ** Examples
> 
> awt_po <- disPo("AWT")
> awt_bg <- disBg("AWT")
> 
> awt_pa_plant <- disPa("AWT", "plant")
> awt_env_plant <- disEnv("AWT", "plant")
> awt_pa_bird <- disPa("AWT", "bird")
> awt_env_bird <- disEnv("AWT", "bird")
> 
> 
> # Or all in one list
> awt <- disData("AWT")
Error in rbind(deparse.level, ...) : 
  numbers of columns of arguments do not match
Calls: disData -> do.call -> <Anonymous> -> rbind
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'spdep'

Packages which this enhances but not available for checking: 'INLA', 'XML'
Namespace in Imports field not imported from: 'rgeos'
  All declared Imports should be used.
Package unavailable to check Rd xrefs: 'spdep'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'png', 'RcppParallel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/disk.frame/disk.frame.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'terra', 'rgdal', 'XML'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dismo/dismo.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'devtools', 'roxygen2'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'Claddis', 'geiger', 'phangorn'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dissUtils/dissUtils.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/distances/distances.Rcheck/00install.out' for details.
Packages suggested but not available for checking: 'devtools', 'kableExtra'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/distcomp/distcomp.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'png', 'xml2'

Package suggested but not available for checking: 'DiagrammeR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'dplyr' 'proxy'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/distory/distory.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/distr6/distr6.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/distrEx/distrEx.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'parallelDist'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'tidyverse'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/DistributionUtils/DistributionUtils.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/distr/distr.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'spelling', 'lintr'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dittodb/dittodb.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'icosa'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/divDyn/divDyn.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/diveMove/diveMove.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespaces in Imports field not imported from:
  'ggmulti' 'loon' 'loon.data' 'loon.ggplot' 'zenplots'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'igraph'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'geiger'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/diversitree/diversitree.Rcheck/00install.out' for details.
Package required but not available: 'rms'

Package suggested but not available for checking: 'BOLTSSIRR'

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

Package suggested but not available for checking: 'rgdal'

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

Packages suggested but not available for checking: 'sendplot', 'HWxtest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/divest/divest.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/divo/divo.Rcheck/00install.out' for details.
Packages required but not available: 'tidyverse', 'kableExtra'

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: 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dixon/dixon.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dixonTest/dixonTest.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'Hmisc', 'xml2'

Package suggested but not available for checking: 'lintr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dkDNA/dkDNA.Rcheck/00install.out' for details.
Package required but not available: 'roll'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dlib/dlib.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dlm/dlm.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/DLMtool/DLMtool.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'hrbrthemes', 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dmbc/dmbc.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/DMCfun/DMCfun.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'rgdal'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'reticulate'
Error(s) in re-building vignettes:
--- re-building 'dMod.Rmd' using rmarkdown
Loading required package: cOde

Attaching package: 'dMod'

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

    profile


Attaching package: 'dplyr'

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

    combine

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

    filter, lag

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

    intersect, setdiff, setequal, union

Warning message:
In system(cmd) : 'make' not found
Warning in system(paste0(R.home(component = "bin"), "/R CMD SHLIB ", filename),  :
  running command 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/R_PACK~1/rinst/bin/x64/R CMD SHLIB jakstat.c' had status 1
Warning in if (class(M) == "matrix") dimM <- dim(M) else dimM <- c(length(M),  :
  the condition has length > 1 and only the first element will be used
Warning in if (class(N) == "matrix") dimN <- dim(N) else dimN <- c(length(N),  :
  the condition has length > 1 and only the first element will be used
Warning message:
In system(cmd) : 'make' not found
Warning in system(paste0(R.home(component = "bin"), "/R CMD SHLIB ", filename),  :
  running command 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/R_PACK~1/rinst/bin/x64/R CMD SHLIB jakstat_s.c' had status 1
Quitting from lines 74-84 (dMod.Rmd) 
Error: processing vignette 'dMod.Rmd' failed with diagnostics:
'initfunc' not loaded  jakstat_s_initmod
--- failed re-building 'dMod.Rmd'

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

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'igraph'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dna/dna.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'RcppParallel'

Package suggested but not available for checking: 'testthis'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'igraph', 'supraHex'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dng/dng.Rcheck/00install.out' for details.
Packages required but not available: 'xml2', 'rvest'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
DNMF: no visible global function definition for 'runif'
NMFpval: no visible global function definition for 'p.adjust'
ndNMF: no visible global function definition for 'runif'
rnk: no visible global function definition for 'write.table'
Undefined global functions or variables:
  p.adjust runif write.table
Consider adding
  importFrom("stats", "p.adjust", "runif")
  importFrom("utils", "write.table")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'igraph', 'arm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'OutliersO3'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'dobin.Rmd' using rmarkdown
Quitting from lines 22-34 (dobin.Rmd) 
Error: processing vignette 'dobin.Rmd' failed with diagnostics:
Package OutliersO3 is needed for the vignette. Please install it.
--- failed re-building 'dobin.Rmd'

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

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'tm', 'quanteda', 'textstem'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/doc2vec/doc2vec.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/docopulae/docopulae.Rcheck/00install.out' for details.
Packages required but not available: 'quanteda', 'quanteda.textstats'

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

Package suggested but not available for checking: 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/documair/documair.Rcheck/00install.out' for details.
Packages required but not available: 'officer', 'xml2'

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

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
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'xml2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'osmdata', 'RcppParallel'

Packages suggested but not available for checking:
  'igraph', 'roxygen2', 'sf', 'tidygraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'FrF2', 'DoE.wrapper'
Packages unavailable to check Rd xrefs: 'FrF2', 'DoE.wrapper'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package which this enhances but not available for checking: 'gurobi'
Codoc mismatches from documentation object 'functionsFromDoE.base':
oa_feasible
  Code: function(nruns, nlevels, strength = 2, verbose = TRUE,
                 returnbound = FALSE)
  Docs: function(nruns, nlevels, strength = 2, verbose = TRUE)
  Argument names in code not in docs:
    returnbound
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'DoE.wrapper'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/DoEstRare/DoEstRare.Rcheck/00install.out' for details.
Package required but not available: 'FrF2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

Package suggested but not available for checking: 'RcmdrMisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking:
  'CPE', 'Hmisc', 'igraph', 'timeROC'
Running examples in 'doMIsaul-Ex.R' failed
The error most likely occurred in:

> ### Name: MultiCons
> ### Title: MultiCons Consensus Clustering Algorithm
> ### Aliases: MultiCons
> 
> ### ** Examples
> 
> library(mclust)
Package 'mclust' version 5.4.7
Type 'citation("mclust")' for citing this R package in publications.
> ### With clustering algorithm choices
> MultiCons(iris[, 1:4],
+           Clustering_selection = c("kmeans", "pam", "DIANA", "MCLUST"),
+           Plot = TRUE)
Loading required namespace: igraph
Failed with error:  'there is no package called 'igraph''
Loading required namespace: RColorBrewer
Loading required namespace: cluster
Error in loadNamespace(x) : there is no package called 'igraph'
Calls: MultiCons ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(doMIsaul)
  > 
  > test_check("doMIsaul")
  Package 'mclust' version 5.4.7
  Type 'citation("mclust")' for citing this R package in publications.
  Loading required namespace: igraph
  Failed with error:  'there is no package called 'igraph''
  Loading required namespace: RColorBrewer
  Loading required namespace: dbscan
  Loading required namespace: cluster
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-seMIsupcox.R:102:3): Evaluation of partitions ───────────────────
  Error: there is no package called 'timeROC'
  Backtrace:
      █
   1. ├─testthat::expect_equal(...) test-seMIsupcox.R:102:2
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. ├─doMIsaul::evaluate_partition_semisup(...)
   5. │ └─doMIsaul:::Extract_AUC(data = data.cc, predictor = "LP", time.vect = timeS)
   6. └─base::loadNamespace(x)
   7.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   8.     └─base:::withOneRestart(expr, restarts[[1L]])
   9.       └─base:::doWithOneRestart(return(expr), restart)
  ── Error (test-unsupMI.R:220:3): multiCOns ─────────────────────────────────────
  Error: there is no package called 'igraph'
  Backtrace:
      █
   1. ├─testthat::expect_equal(...) test-unsupMI.R:220:2
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. ├─doMIsaul::MultiCons(...)
   5. └─base::loadNamespace(x)
   6.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   7.     └─base:::withOneRestart(expr, restarts[[1L]])
   8.       └─base:::doWithOneRestart(return(expr), restart)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 71 ]
  Error: Test failures
  Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'rvest', 'xml2'
Note: found 100 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'rvest', 'xml2'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'devtools', 'roxygen2'
Namespace in Imports field not imported from: 'gridExtra'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'doRedis', 'devtools'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'igraph'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dosearch/dosearch.Rcheck/00install.out' for details.
Package required but not available: 'latticeExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/DoseFinding/DoseFinding.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'rms'
Error(s) in re-building vignettes:
--- re-building 'dosresmeta.Rnw' using knitr
Quitting from lines 330-331 (dosresmeta.Rnw) 
Error: processing vignette 'dosresmeta.Rnw' failed with diagnostics:
there is no package called 'rms'
--- failed re-building 'dosresmeta.Rnw'

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

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
dostats: no visible binding for global variable 'na.fail'
first: no visible global function definition for 'head'
last: no visible global function definition for 'tail'
pval.default: no visible global function definition for '.hasSlot'
pval.lm: no visible global function definition for 'anova'
Undefined global functions or variables:
  .hasSlot anova head na.fail tail
Consider adding
  importFrom("methods", ".hasSlot")
  importFrom("stats", "anova", "na.fail")
  importFrom("utils", "head", "tail")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'roxygen2'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dotCall64/dotCall64.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/DOVE/DOVE.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'xml2'
'LazyData' is specified without a 'data' directory
Running examples in 'downlit-Ex.R' failed
The error most likely occurred in:

> ### Name: downlit_html_path
> ### Title: Syntax highlight and link an HTML page
> ### Aliases: downlit_html_path downlit_html_node
> 
> ### ** Examples
> 
> node <- xml2::read_xml("<p><code>base::t()</code></p>")
Error in loadNamespace(x) : there is no package called 'xml2'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(downlit)
  > 
  > test_check("downlit")
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (9)
  • On Windows (2)
  • rmarkdown::pandoc_version() > "2.0.0" is not TRUE (3)
  • rmarkdown::pandoc_version() >= "2.10" is not TRUE (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-downlit-html.R:12:3): highlight all pre inside div.downlit ──────
  Error: there is no package called 'xml2'
  Backtrace:
      █
   1. └─base::loadNamespace(x) test-downlit-html.R:12:2
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base:::withOneRestart(expr, restarts[[1L]])
   4.       └─base:::doWithOneRestart(return(expr), restart)
  ── Error (test-downlit-html.R:26:3): special package string gets linked ────────
  Error: there is no package called 'xml2'
  Backtrace:
      █
   1. └─base::loadNamespace(x) test-downlit-html.R:26:2
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base:::withOneRestart(expr, restarts[[1L]])
   4.       └─base:::doWithOneRestart(return(expr), restart)
  
  [ FAIL 2 | WARN 0 | SKIP 15 | PASS 101 ]
  Error: Test failures
  Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'keras', 'tensorflow', 'rgdal'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'alakazam', 'phangorn', 'shazam'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'devtools'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dparser/dparser.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dpcc/dpcc.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dpcid/dpcid.Rcheck/00install.out' for details.
Package required but not available: 'rlist'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'png', 'XML'

Packages suggested but not available for checking: 'Cairo', 'tikzDevice'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dplyr/dplyr.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'devtools'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/DPP/DPP.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'graphics'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/DPQ/DPQ.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dpseg/dpseg.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'MASS'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/DPWeibull/DPWeibull.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dqrng/dqrng.Rcheck/00install.out' for details.
Packages suggested but not available for checking: 'devtools', 'roxygen2'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'spelling'

Package which this enhances but not available for checking: 'rgl'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dracor/dracor.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'golem', 'igraph', 'xml2', 'rvest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 100 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

Packages suggested but not available for checking:
  'ggraph', 'keras', 'networkD3', 'qs'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'xml2'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
DRaWR: no visible global function definition for 'write.table'
DRaWR: no visible global function definition for 'read.table'
DRaWR: no visible global function definition for 'aggregate'
DRaWR: no visible global function definition for 'slot'
Undefined global functions or variables:
  aggregate read.table slot write.table
Consider adding
  importFrom("methods", "slot")
  importFrom("stats", "aggregate")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespaces in Imports field not imported from:
  'magrittr' 'purrr' 'rlang'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'rstan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'spelling'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'spelling'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'DiagrammeR'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/drf/drf.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/drgee/drgee.Rcheck/00install.out' for details.
Package required but not available: 'spdep'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/DriftBurstHypothesis/DriftBurstHypothesis.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'devtools', 'roxygen2'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/DrImpute/DrImpute.Rcheck/00install.out' for details.
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/DRIP/DRIP.Rcheck/00install.out' for details.
Packages required but not available: 'mlr', 'iml'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'GenomicFeatures', 'TxDb.Hsapiens.UCSC.hg19.knownGene',
  'org.Hs.eg.db'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/drmdel/drmdel.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'vdiffr'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(droll)
  > 
  > test_check("droll")
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-plot.R:3:3): plotting functions work ────────────────────────────
  Error: there is no package called 'vdiffr'
  Backtrace:
      █
   1. └─base::loadNamespace(x) test-plot.R:3:2
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base:::withOneRestart(expr, restarts[[1L]])
   4.       └─base:::doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 186 ]
  Deleting unused snapshots:
  * _snaps/plot/gd.svg
  * _snaps/plot/gp.svg
  * _snaps/plot/gq.svg
  * _snaps/plot/gr.svg
  Error: Test failures
  Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'DESeq2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
compute_xsq: no visible global function definition for 'chisq.test'
Undefined global functions or variables:
  chisq.test
Consider adding
  importFrom("stats", "chisq.test")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'spelling'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'XML'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'stR'
Namespaces in Imports field not imported from:
  'rJava' 'tools'
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building 'dsa-vignette.Rmd' using rmarkdown
Quitting from lines 281-297 (dsa-vignette.Rmd) 
Error: processing vignette 'dsa-vignette.Rmd' failed with diagnostics:
there is no package called 'stR'
--- failed re-building 'dsa-vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
DSBayes: no visible global function definition for 'qnorm'
DSBayes: no visible global function definition for 'coef'
DSBayes: no visible global function definition for 'vcov'
DSBayes : MLE: no visible global function definition for 'qnorm'
DSBayes: no visible global function definition for 'integrate'
DSBayes : qfunc.numer : <anonymous>: no visible global function
  definition for 'dnorm'
DSBayes : ds.numer: no visible global function definition for
  'integrate'
DSBayes : lower: no visible global function definition for 'qlogis'
DSBayes : lower: no visible global function definition for 'integrate'
DSBayes : upper: no visible global function definition for 'qlogis'
DSBayes : upper: no visible global function definition for 'integrate'
DSBayes: no visible global function definition for 'optimize'
DSBayes: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  coef dnorm integrate optimize qlogis qnorm uniroot vcov
Consider adding
  importFrom("stats", "coef", "dnorm", "integrate", "optimize", "qlogis",
             "qnorm", "uniroot", "vcov")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'spelling'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'kableExtra'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dscore/dscore.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dse/dse.Rcheck/00install.out' for details.
Packages required but not available: 'dssd', 'sf'

Package suggested but not available for checking: 'lwgeom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Note: found 149 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Note: found 4891 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dslice/dslice.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'hive'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/DSL/DSL.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'spelling'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dsmisc/dsmisc.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'dsBaseClient'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'sf', 'rgdal'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/DstarM/DstarM.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'igraph'
Error(s) in re-building vignettes:
--- re-building 'Captain_Example.Rmd' using rmarkdown
Quitting from lines 220-558 (Captain_Example.Rmd) 
Error: processing vignette 'Captain_Example.Rmd' failed with diagnostics:
object 'captain_hgm' not found
--- failed re-building 'Captain_Example.Rmd'

--- re-building 'Introduction_to_Belief_Functions.Rmd' using rmarkdown
Quitting from lines 192-202 (Introduction_to_Belief_Functions.Rmd) 
Error: processing vignette 'Introduction_to_Belief_Functions.Rmd' failed with diagnostics:
could not find function "graph_from_incidence_matrix"
--- failed re-building 'Introduction_to_Belief_Functions.Rmd'

--- re-building 'The_Monty_Hall_Game.Rmd' using rmarkdown
Quitting from lines 188-199 (The_Monty_Hall_Game.Rmd) 
Error: processing vignette 'The_Monty_Hall_Game.Rmd' failed with diagnostics:
could not find function "graph_from_incidence_matrix"
--- failed re-building 'The_Monty_Hall_Game.Rmd'

--- re-building 'Zadeh_Example.Rmd' using rmarkdown
Quitting from lines 170-198 (Zadeh_Example.Rmd) 
Error: processing vignette 'Zadeh_Example.Rmd' failed with diagnostics:
object 'meddiag_hgm' not found
--- failed re-building 'Zadeh_Example.Rmd'

SUMMARY: processing the following files failed:
  'Captain_Example.Rmd' 'Introduction_to_Belief_Functions.Rmd'
  'The_Monty_Hall_Game.Rmd' 'Zadeh_Example.Rmd'

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'pec', 'Ecdat'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/DSWE/DSWE.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Note: found 1 marked Latin-1 string
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'Hmisc'

Package suggested but not available for checking: 'latticeExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
DLR: no visible global function definition for 'formula'
DLR: no visible global function definition for 'terms'
DLR: no visible global function definition for 'model.matrix'
DLR: no visible global function definition for 'as.formula'
DLR: no visible binding for global variable 'binomial'
DLR: no visible global function definition for 'coef'
DLR: no visible global function definition for 'pnorm'
DLR: no visible global function definition for 'qnorm'
acc.1test: no visible global function definition for 'qnorm'
pv.gs: no visible global function definition for 'pchisq'
pv.rpv: no visible global function definition for 'qnorm'
pv.rpv: no visible global function definition for 'pnorm'
pv.wgs: no visible global function definition for 'pchisq'
sesp.diff.ci: no visible global function definition for 'qnorm'
sesp.mcnemar: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  as.formula binomial coef formula model.matrix pchisq pnorm qnorm
  terms
Consider adding
  importFrom("stats", "as.formula", "binomial", "coef", "formula",
             "model.matrix", "pchisq", "pnorm", "qnorm", "terms")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/DTDA.cif/DTDA.cif.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/DtD/DtD.Rcheck/00install.out' for details.
Package required but not available: 'rgl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
DTK.plot: no visible global function definition for 'axis'
DTK.plot: no visible global function definition for 'title'
DTK.plot: no visible global function definition for 'lines'
DTK.plot: no visible global function definition for 'points'
DTK.test: no visible binding for global variable 'sd'
DTK.test: no visible global function definition for 'qtukey'
TK.test: no visible global function definition for 'TukeyHSD'
TK.test: no visible global function definition for 'aov'
Undefined global functions or variables:
  TukeyHSD aov axis lines points qtukey sd title
Consider adding
  importFrom("graphics", "axis", "lines", "points", "title")
  importFrom("stats", "TukeyHSD", "aov", "qtukey", "sd")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
DTMC: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dtrSurv/dtrSurv.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'rlist'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dtw/dtw.Rcheck/00install.out' for details.
Package required but not available: 'rgdal'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dualtrees/dualtrees.Rcheck/00install.out' for details.
Namespaces in Imports field not imported from:
  'digest' 'dplyr'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'Seurat'

Package suggested but not available for checking: 'hdf5r'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/duckdb/duckdb.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
File
  LICENSE
is not mentioned in the DESCRIPTION file.
dummy: no visible global function definition for 'model.matrix'
dummy: no visible global function definition for 'model.frame'
Undefined global functions or variables:
  model.frame model.matrix
Consider adding
  importFrom("stats", "model.frame", "model.matrix")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Note: found 2854 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
cvSDDT: no visible global function definition for 'qt'
cvSDDT : Cj_SD.fun: no visible global function definition for 'combn'
cvSDDT: no visible global function definition for 'uniroot'
cvSUDT: no visible global function definition for 'rnorm'
cvSUDT: no visible global function definition for 'rchisq'
cvSUDT : psi.fun: no visible global function definition for 'pnorm'
cvSUDT: no visible global function definition for 'qt'
cvSUDT: no visible global function definition for 'uniroot'
cvSUDT: no visible global function definition for 'combn'
nvDT : samplesize: no visible global function definition for 'rnorm'
nvDT : samplesize: no visible global function definition for 'rchisq'
nvDT : samplesize: no visible global function definition for 'pnorm'
nvDT : ssBonf: no visible global function definition for 'qnorm'
nvDT : ssBonf: no visible global function definition for 'qt'
nvDT : ssBonf: no visible global function definition for 'rnorm'
nvDT : ssBonf: no visible global function definition for 'rchisq'
nvDT : ssBonf: no visible global function definition for 'pnorm'
nvDT: no visible global function definition for 'uniroot'
powDT: no visible global function definition for 'rnorm'
powDT: no visible global function definition for 'rchisq'
powDT: no visible global function definition for 'pnorm'
qvSDDT: no visible global function definition for 'pt'
qvSUDT: no visible global function definition for 'rnorm'
qvSUDT: no visible global function definition for 'rchisq'
qvSUDT : psi.fun: no visible global function definition for 'pnorm'
qvSUDT: no visible global function definition for 'pt'
qvSUDT : Pj.fun: no visible global function definition for 'qt'
qvSUDT : Pj.fun: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  combn pnorm pt qnorm qt rchisq rnorm uniroot
Consider adding
  importFrom("stats", "pnorm", "pt", "qnorm", "qt", "rchisq", "rnorm",
             "uniroot")
  importFrom("utils", "combn")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Clough: no visible global function definition for 'dgamma'
computePosterior,Counts: no visible global function definition for
  'dnbinom'
getPosteriorParam,Counts: no visible global function definition for
  'qgamma'
getPosteriorParam,Counts: no visible global function definition for
  'dgamma'
getPosteriorParam,Counts: no visible global function definition for
  'pgamma'
plotPosterior,Counts: no visible global function definition for 'axis'
plotPosterior,Counts: no visible global function definition for
  'abline'
plotPosterior,Counts: no visible global function definition for 'lines'
plotPosterior,Counts: no visible global function definition for 'rect'
plotPosterior,Counts: no visible global function definition for 'curve'
plotPosterior,Counts: no visible global function definition for
  'dgamma'
plotPosterior,Counts: no visible global function definition for
  'legend'
show,Counts: no visible global function definition for 'head'
show,Counts: no visible global function definition for 'tail'
Undefined global functions or variables:
  abline axis curve dgamma dnbinom head legend lines pgamma qgamma rect
  tail
Consider adding
  importFrom("graphics", "abline", "axis", "curve", "legend", "lines",
             "rect")
  importFrom("stats", "dgamma", "dnbinom", "pgamma", "qgamma")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'lintr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/durmod/durmod.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'DT'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'tab'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'rgdal'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dwdradar/dwdradar.Rcheck/00install.out' for details.
Package required but not available: 'hglasso'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'Ecdat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/DynamicGP/DynamicGP.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dynamichazard/dynamichazard.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'png', 'ari'

Package suggested but not available for checking: 'imager'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dynaTree/dynaTree.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
MultiTestH0 : MultiTestOneColumn: no visible global function definition
  for 'pchisq'
RunClustering : CheckClusterNew: no visible global function definition
  for 'qchisq'
RunClustering: no visible global function definition for 'qchisq'
RunDenoising: no visible binding for global variable 'var'
RunDenoising: no visible global function definition for 'qchisq'
RunDenoising: no visible binding for global variable 'median'
RunDenoising: no visible global function definition for 'var'
RunDenoising : buildEstimate: no visible global function definition for
  'qchisq'
Undefined global functions or variables:
  median pchisq qchisq var
Consider adding
  importFrom("stats", "median", "pchisq", "qchisq", "var")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

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
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'dynutils', 'lmds'

Packages suggested but not available for checking:
  'diffusionMap', 'igraph', 'smacof'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dynutils', 'ggraph', 'GillespieSSA2', 'igraph', 'lmds', 'tidygraph'

Packages suggested but not available for checking:
  'anndata', 'dynwrap', 'Seurat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
GetIntMod: no visible global function definition for 'arima'
GetLikeDI: no visible global function definition for 'arima'
GetLikeDI: no visible global function definition for 'logLik'
GetPV: no visible global function definition for 'optimize'
GetPV: no visible global function definition for 'pchisq'
fitdi: no visible global function definition for 'optimize'
Undefined global functions or variables:
  arima logLik optimize pchisq
Consider adding
  importFrom("stats", "arima", "logLik", "optimize", "pchisq")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dynmix/dynmix.Rcheck/00install.out' for details.
Package required but not available: 'rms'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'dynutils'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'dynutils', 'dynfeature', 'dyndimred', 'dynwrap', 'ggraph', 'igraph',
  'tidygraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dynpred/dynpred.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'roxygen2'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dynr/dynr.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dynsbm/dynsbm.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/dynsurv/dynsurv.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'proxyC'

Package suggested but not available for checking: 'hdf5r'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'babelwhale', 'dynutils', 'dynparam', 'igraph'

Packages suggested but not available for checking: 'dyndimred', 'hdf5r'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 9 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/DysPIA/DysPIA.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/e1071/e1071.Rcheck/00install.out' for details.
Package required but not available: 'accelerometry'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/eaf/eaf.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/Eagle/Eagle.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/EAinference/EAinference.Rcheck/00install.out' for details.
Packages required but not available: 'energyr', 'leaflet', 'shinytest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'vdiffr', 'roxygen2'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Malformed Description field: should contain one or more complete sentences.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/earth/earth.Rcheck/00install.out' for details.
Package required but not available: 'RcppParallel'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/EasyABC/EasyABC.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'vdiffr', 'pkgdown'
Namespace in Imports field not imported from: 'progress'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespaces in Imports field not imported from:
  'ggplot2' 'reshape2' 'scales' 'xtable'
  All declared Imports should be used.
Packages in Depends field not imported from:
  'base64enc' 'knitr' 'markdown'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.file_attachment: no visible global function definition for
  'base64encode'
.plot_attachment: no visible global function definition for 'dev.off'
.update_list: no visible global function definition for 'modifyList'
easyHtmlReport: no visible global function definition for 'knit'
easyHtmlReport: no visible global function definition for
  'markdownToHTML'
mime_part.data.frame: no visible global function definition for
  'write.table'
mime_part.ggplot: no visible binding for global variable 'pdf'
mime_part.matrix: no visible global function definition for
  'write.table'
mime_part.trellis: no visible binding for global variable 'pdf'
simpleHtmlReport : <anonymous>: no visible global function definition
  for 'write.table'
Undefined global functions or variables:
  base64encode dev.off knit markdownToHTML modifyList pdf write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("utils", "modifyList", "write.table")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'OpenMx'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'Hmisc', 'XML'

Package suggested but not available for checking: 'qs'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/easyVerification/easyVerification.Rcheck/00install.out' for details.
Package which this enhances but not available for checking: 'gurobi'
Namespace in Imports field not imported from: 'mathjaxr'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'RSQLite'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'kableExtra', 'devtools'
Namespace in Imports field not imported from: 'knitr'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
eb: no visible global function definition for 'optimize'
ebalance: no visible global function definition for 'var'
Undefined global functions or variables:
  optimize var
Consider adding
  importFrom("stats", "optimize", "var")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'spelling'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/EBEN/EBEN.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/EBglmnet/EBglmnet.Rcheck/00install.out' for details.
Packages required but not available: 'rgdal', 'sf', 'xml2'

Package suggested but not available for checking: 'rnaturalearth'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ebmstate/ebmstate.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'roxygen2'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/eBsc/eBsc.Rcheck/00install.out' for details.
ebSNP: no visible global function definition for 'optim'
Undefined global functions or variables:
  optim
Consider adding
  importFrom("stats", "optim")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'INLA'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/eCAR/eCAR.Rcheck/00install.out' for details.
Packages required but not available: 'rsdmx', 'xml2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ECctmc/ECctmc.Rcheck/00install.out' for details.
Package required but not available: 'Ecfun'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'roxygen2'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ecespa/ecespa.Rcheck/00install.out' for details.
Packages required but not available: 'jpeg', 'xml2', 'rvest'

Packages suggested but not available for checking:
  'Ecdat', 'ipumsr', 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ECGofTestDx/ECGofTestDx.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'leaflet'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Error: package or namespace load failed for 'echarty':
 .onLoad failed in loadNamespace() for 'echarty', details:
  call: loadNamespace(x)
  error: there is no package called 'shiny'
Execution halted

It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'sf'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking:
  'ggspatial', 'kableExtra', 'sf'
Error(s) in re-building vignettes:
--- re-building 'introduction.Rmd' using rmarkdown
Quitting from lines 13-44 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'introduction.Rmd'

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

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'geouy'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'WGCNA'

Package suggested but not available for checking: 'ComplexHeatmap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'lmtest' 'sandwich' 'urca'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available:
  'sf', 'gdalUtils', 'rgdal', 'gdalUtilities', 'rvest', 'xml2',
  'rasterDT'

Package suggested but not available for checking: 'rasterVis'

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

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'devtools'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ecodist/ecodist.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'XML'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'sf'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'seacarb'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ecolMod/ecolMod.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

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: 'igraph', 'intergraph'

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

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

Package suggested but not available for checking: 'ggraph'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ECOSolveR/ECOSolveR.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'biomod2', 'rms'

Packages suggested but not available for checking: 'rgdal', 'XML', 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'graphics'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'qgraph', 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'Hmisc'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'smacof'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ecotraj/ecotraj.Rcheck/00install.out' for details.
Package required but not available: 'XML'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'ggraph', 'igraph'
Running examples in 'ecpc-Ex.R' failed
The error most likely occurred in:

> ### Name: visualiseGroupset
> ### Title: Visualise a group set
> ### Aliases: visualiseGroupset
> 
> ### ** Examples
> 
> #groups without hierarchical constraints
> groupset <- list("Group1"=c(1:20),"Group2"=c(15,30))
> visualiseGroupset(groupset,c(0.5,2))
Loading required namespace: ggplot2
Loading required namespace: ggraph
Failed with error:  'there is no package called 'ggraph''
Loading required namespace: igraph
Failed with error:  'there is no package called 'igraph''
Error in visualiseGroupset(groupset, c(0.5, 2)) : 
  Packages ggplot2, ggraph, igraph and scales should be installed
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ecp/ecp.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ecr/ecr.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'spdep', 'sf', 'tmap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package in Depends field not imported from: 'spc'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/edci/edci.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/eddington/eddington.Rcheck/00install.out' for details.
Package required but not available: 'rgdal'

Package suggested but not available for checking: 'sf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'tm', 'XML'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'xml2'

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

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

Package suggested but not available for checking: 'tidygraph'

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

Package suggested but not available for checking: 'huge'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
UCexactTest: no visible global function definition for 'is'
UCexactTest: no visible global function definition for 'new'
pvalue: no visible global function definition for 'dnbinom'
pvalue: no visible global function definition for 'pnbinom'
sup.mu: no visible global function definition for 'predict'
Undefined global functions or variables:
  dnbinom is new pnbinom predict
Consider adding
  importFrom("methods", "is", "new")
  importFrom("stats", "dnbinom", "pnbinom", "predict")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/edina/edina.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespaces in Imports field not imported from:
  'dplyr' 'magrittr' 'tibble'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package unavailable to check Rd xrefs: 'ndl'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/eDMA/eDMA.Rcheck/00install.out' for details.
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/EDMeasure/EDMeasure.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'rgl'

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.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'rgdal'

Packages suggested but not available for checking:
  'tidyverse', 'spelling', 'ggmap'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
geteegdata: no visible global function definition for 'untar'
geteegdata: no visible global function definition for 'read.table'
geteegdata: no visible global function definition for 'write.csv'
geteegdata: no visible global function definition for 'write.table'
Undefined global functions or variables:
  read.table untar write.csv write.table
Consider adding
  importFrom("utils", "read.table", "untar", "write.csv", "write.table")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'rgl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'nnfor'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'rlist'

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.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'PCovR'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/EFAtools/EFAtools.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'pcalg', 'igraph'

Package suggested but not available for checking: 'qgraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'rmarkdown'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking:
  'brms', 'mediation', 'rms', 'rstanarm', 'rstantools', 'spelling'
Package unavailable to check Rd xrefs: 'rstantools'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Malformed Title field: should not end in a period.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ef/ef.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Note: found 24 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available:
  'qgraph', 'semPlot', 'igraph', 'NetworkToolbox'

Packages suggested but not available for checking:
  'kableExtra', 'OpenMx', 'wTO'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'rstan', 'StanHeaders'

Package suggested but not available for checking: 'eggCountsExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'png'
Error(s) in re-building vignettes:
--- re-building 'Ecosystem.Rmd' using rmarkdown
Loading required package: ggplot2
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Bin width defaults to 1/30 of the range of the data. Pick better value with `binwidth`.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Bin width defaults to 1/30 of the range of the data. Pick better value with `binwidth`.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Bin width defaults to 1/30 of the range of the data. Pick better value with `binwidth`.
Bin width defaults to 1/30 of the range of the data. Pick better value with `binwidth`.
Bin width defaults to 1/30 of the range of the data. Pick better value with `binwidth`.
Bin width defaults to 1/30 of the range of the data. Pick better value with `binwidth`.
Bin width defaults to 1/30 of the range of the data. Pick better value with `binwidth`.
--- finished re-building 'Ecosystem.Rmd'

--- re-building 'Overview.Rmd' using rmarkdown
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Bin width defaults to 1/30 of the range of the data. Pick better value with `binwidth`.
adding dummy grobs
adding dummy grobs
Quitting from lines 197-215 (Overview.Rmd) 
Error: processing vignette 'Overview.Rmd' failed with diagnostics:
there is no package called 'png'
--- failed re-building 'Overview.Rmd'

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

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'tidygraph'

Package suggested but not available for checking: 'igraph'

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

Package suggested but not available for checking: 'pkgdown'

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

Packages suggested but not available for checking:
  'EGRETci', 'pkgdown', 'png'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/eha/eha.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'vegdata'
Error(s) in re-building vignettes:
--- re-building 'eHOF.Rnw' using knitr
Quitting from lines 36-45 (eHOF.Rnw) 
Error: processing vignette 'eHOF.Rnw' failed with diagnostics:
there is no package called 'vegdata'
--- failed re-building 'eHOF.Rnw'

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

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'devtools'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'XML'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'igraph'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/eicm/eicm.Rcheck/00install.out' for details.
Packages required but not available: 'wru', 'sf', 'leaflet'

Package suggested but not available for checking: 'tigris'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
eiginv: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
boot_pr_comp: no visible global function definition for 'cov'
boot_pr_comp: no visible global function definition for 'quantile'
boot_pr_comp: no visible global function definition for 'segments'
boot_pr_comp: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline cov quantile segments
Consider adding
  importFrom("graphics", "abline", "segments")
  importFrom("stats", "cov", "quantile")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/EigenR/EigenR.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Malformed Description field: should contain one or more complete sentences.
Packages in Depends field not imported from:
  'class' 'quantreg'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
cluster.segment: no visible global function definition for 'kmeans'
cluster.segment: no visible global function definition for 'knn'
comp.anc.dist: no visible global function definition for 'wilcox.test'
eila: no visible global function definition for 'hasArg'
get.prob.score: no visible global function definition for 'glm'
get.prob.score: no visible global function definition for 'binomial'
get.prob.score: no visible binding for global variable 'logit'
get.prob.score: no visible global function definition for 'predict'
quantreg.est: no visible global function definition for 'rnorm'
quantreg.est: no visible global function definition for 'rq.fit.fnb'
Undefined global functions or variables:
  binomial glm hasArg kmeans knn logit predict rnorm rq.fit.fnb
  wilcox.test
Consider adding
  importFrom("methods", "hasArg")
  importFrom("stats", "binomial", "glm", "kmeans", "predict", "rnorm",
             "wilcox.test")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/eimpute/eimpute.Rcheck/00install.out' for details.
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/einsum/einsum.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/eiPack/eiPack.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'rgl'
Running examples in 'ei-Ex.R' failed
The error most likely occurred in:

> ### Name: tomogRxC3d
> ### Title: Plotting 2x3 Ecological Inference Estimates in 3 dimensions
> ### Aliases: tomogRxC3d
> 
> ### ** Examples
> 
> data(RxCdata)
> formula <- cbind(turnout, noturnout) ~ cbind(white, black, hisp)
> tomogRxC3d(formula, RxCdata, total=NULL, lci=TRUE, estimates=TRUE, ci=TRUE, transparency=.5, 
+ 	light=FALSE, rotate=FALSE)
Error: Package rgl is needed for the tomogRxC3d function to work. Please install it.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/eive/eive.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'sf'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'qgraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/elec.strat/elec.strat.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'stats'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'devtools', 'gnumeric', 'readODS'

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: 'rgdal'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/elfDistr/elfDistr.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'devtools', 'pkgdown'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ellipsis/ellipsis.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'datasets'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/elmNNRcpp/elmNNRcpp.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/EloChoice/EloChoice.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/EloRating/EloRating.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/elo/elo.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/EL/EL.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/elsa/elsa.Rcheck/00install.out' for details.
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: 'parallel'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Likelihood: no visible global function definition for
  'makePSOCKcluster'
Likelihood: no visible global function definition for 'clusterExport'
Likelihood: no visible global function definition for 'makeForkCluster'
Likelihood.first.run: no visible global function definition for
  'clusterApply'
Likelihood.next.runs: no visible global function definition for
  'clusterApply'
es.stopCluster: no visible global function definition for 'stopCluster'
plot.es.pedigree: no visible global function definition for 'hasArg'
Undefined global functions or variables:
  clusterApply clusterExport hasArg makeForkCluster makePSOCKcluster
  stopCluster
Consider adding
  importFrom("methods", "hasArg")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'latticeExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ELYP/ELYP.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'xml2'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'move', 'rgl'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/EMbC/EMbC.Rcheck/00install.out' for details.
Packages required but not available: 'keras', 'tensorflow'

Package suggested but not available for checking: 'rstanarm'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 62 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package which this enhances but not available for checking: 'PPtree'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/EMCluster/EMCluster.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/EMC/EMC.Rcheck/00install.out' for details.
Package required but not available: 'nnfor'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'rgl'
Package unavailable to check Rd xrefs: 'rgl'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'readODS', 'saeRobust', 'spdep'

Package suggested but not available for checking: 'simFrame'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/emdist/emdist.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/EMD/EMD.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/emIRT/emIRT.Rcheck/00install.out' for details.
Packages required but not available: 'units', 'sf', 'rgdal'

Packages suggested but not available for checking:
  'osmar', 'eixport', 'lwgeom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'xml2'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'xml2', 'emld'

Packages suggested but not available for checking:
  'EML', 'units', 'spelling'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'clusterSim'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to 'reshape' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'reshape'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
MFFetch: no visible global function definition for 'melt'
Undefined global functions or variables:
  melt
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'brms', 'mediation'

Packages which this enhances but not available for checking:
  'CARBayes', 'rstanarm'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/EMMIXgene/EMMIXgene.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/EMMIXmfa/EMMIXmfa.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/emoa/emoa.Rcheck/00install.out' for details.
Packages required but not available: 'showtext', 'sysfonts'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 9451 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'spelling'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/empichar/empichar.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'DESeq2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/emplik/emplik.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'rms'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/emstreeR/emstreeR.Rcheck/00install.out' for details.
ExactMultinomialTest: no visible global function definition for
  'dmultinom'
ExactMultinomialTest : <anonymous>: no visible global function
  definition for 'dmultinom'
ExactMultinomialTestChisquare : <anonymous>: no visible global function
  definition for 'dmultinom'
MonteCarloMultinomialTest: no visible global function definition for
  'rmultinom'
MonteCarloMultinomialTest: no visible global function definition for
  'flush.console'
MonteCarloMultinomialTestChisquare: no visible global function
  definition for 'rmultinom'
MonteCarloMultinomialTestChisquare: no visible global function
  definition for 'flush.console'
multinomial.test: no visible global function definition for
  'flush.console'
plotMultinom: no visible global function definition for 'barplot'
plotMultinom: no visible global function definition for 'mtext'
Undefined global functions or variables:
  barplot dmultinom flush.console mtext rmultinom
Consider adding
  importFrom("graphics", "barplot", "mtext")
  importFrom("stats", "dmultinom", "rmultinom")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/EMVS/EMVS.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/eNchange/eNchange.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/enc/enc.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'knitr'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/endogMNP/endogMNP.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/endorse/endorse.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/energy/energy.Rcheck/00install.out' for details.
Package required but not available: 'RgoogleMaps'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'rangeModelMetadata'

Packages suggested but not available for checking:
  'spocc', 'rasterVis', 'sf', 'blockCV', 'devtools', 'latticeExtra'

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

Packages suggested but not available for checking:
  'hypervolume', 'leaflet', 'ecospat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/enRich/enRich.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'kknn'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'EnsembleBase'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'EnsembleBase'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespaces in Imports field not imported from:
  'Biostrings' 'DECIPHER' 'ggplot2' 'reshape2' 'usethis'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespaces in Imports field not imported from:
  'RCurl' 'bitops' 'rjson'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'pkgdown'
Namespaces in Imports field not imported from:
  'SPECIES' 'ade4'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/EntropyEstimation/EntropyEstimation.Rcheck/00install.out' for details.
diffcv: no visible global function definition for 'sd'
diffcvall: no visible global function definition for 'sd'
diffcvall: no visible global function definition for 'fligner.test'
diffcvall: no visible global function definition for 'p.adjust'
diffcvpFK: no visible global function definition for 'fligner.test'
diffcvpFK: no visible global function definition for 'p.adjust'
diffexp: no visible global function definition for 'var'
diffexp: no visible global function definition for 't.test'
diffexp: no visible global function definition for 'p.adjust'
diffexp2: no visible global function definition for 'var'
diffexp2: no visible global function definition for 't.test'
diffexp2: no visible global function definition for 'p.adjust'
diffnsepperm: no visible global function definition for 'p.adjust'
diffseall: no visible global function definition for 'p.adjust'
Undefined global functions or variables:
  fligner.test p.adjust sd t.test var
Consider adding
  importFrom("stats", "fligner.test", "p.adjust", "sd", "t.test", "var")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/EntropyMCMC/EntropyMCMC.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/EnvCpt/EnvCpt.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'xcms', 'MSnbase'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/enviPat/enviPat.Rcheck/00install.out' for details.
Package required but not available: 'readMzXmlData'

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

Package suggested but not available for checking: 'spelling'

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

Package suggested but not available for checking: 'rgdal'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/EnviroStat/EnviroStat.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/envnames/envnames.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'openair'
'LazyData' is specified without a 'data' directory
Running examples in 'envoutliers-Ex.R' failed
The error most likely occurred in:

> ### Name: KRDetect.outliers.EV
> ### Title: Identification of outliers using extreme value theory
> ### Aliases: KRDetect.outliers.EV
> 
> ### ** Examples
> 
> data("mydata", package = "openair")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called 'openair'
Calls: data -> find.package
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package unavailable to check Rd xrefs: 'Hmisc'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'officer', 'rvg', 'flextable'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'Hmisc'
'library' or 'require' call to 'plotrix' which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  'Hmisc' 'survival'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'plotrix'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'a.alpha.ade' 'a.coladd.ade' 'a.getcol.ade' 'a.glc'
Running examples in 'epade-Ex.R' failed
The error most likely occurred in:

> ### Name: box.plot.wtd
> ### Title: weighted Boxplot
> ### Aliases: box.plot.wtd
> ### Keywords: boxplot
> 
> ### ** Examples
> 
> x<-rnorm(1000)
> g<-round(runif(1000))
> w<-abs(rnorm(1000))
> d<- data.frame(x, g, w)
> box.plot.wtd('x', 'g', w='w', data=d)
Error in library(Hmisc) : there is no package called 'Hmisc'
Calls: box.plot.wtd -> library
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/epanet2toolkit/epanet2toolkit.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'imager', 'tidyverse'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available:
  'tidyverse', 'leaflet', 'rvest', 'xml2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'igraph', 'threejs'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/EpiContactTrace/EpiContactTrace.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'tibble'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'rvest', 'xml2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'vdiffr'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'knitr'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'epicontacts', 'leaflet', 'ggmap'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'roxygen2', 'spelling', 'devtools', 'pkgdown', 'lintr', 'igraph'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'kableExtra'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/EpiILM/EpiILM.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'epidict'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'imputeTS'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/EpiModel/EpiModel.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/epinet/epinet.Rcheck/00install.out' for details.
Package required but not available: 'igraph'

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

Packages suggested but not available for checking:
  'EpiSoon', 'kableExtra', 'rnaturalearth', 'rstantools', 'spelling'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'spdep'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/epiphy/epiphy.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/Epi/Epi.Rcheck/00install.out' for details.
Packages required but not available: 'officer', 'flextable', 'png'

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

--- re-building 'epiR_descriptive.Rmd' using rmarkdown
Loading required package: survival
Package epiR 2.0.35 is loaded
Type help(epi.about) for summary information
Type browseVignettes(package = 'epiR') to learn how to use epiR for applied epidemiological analyses



Attaching package: 'lubridate'

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

    date, intersect, setdiff, union

To access larger datasets in this package, install the spDataLarge
package with: `install.packages('spDataLarge',
repos='https://nowosad.github.io/drat/', type='source')`
Loading required package: sp
rgeos version: 0.5-7, (SVN revision 676)
 GEOS runtime version: 3.9.1-CAPI-1.14.2 
 Please note that rgeos will be retired by the end of 2023,
plan transition to sf functions using GEOS at your earliest convenience.
 GEOS using OverlayNG
 Linking to sp version: 1.4-5 
 Polygon checking: TRUE 

Quitting from lines 266-271 (epiR_descriptive.Rmd) 
Error: processing vignette 'epiR_descriptive.Rmd' failed with diagnostics:
there is no package called 'rgdal'
--- failed re-building 'epiR_descriptive.Rmd'

--- re-building 'epiR_measures_of_association.Rmd' using rmarkdown
Quitting from lines 19-22 (epiR_measures_of_association.Rmd) 
Error: processing vignette 'epiR_measures_of_association.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'epiR_measures_of_association.Rmd'

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

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

SUMMARY: processing the following files failed:
  'epiR_descriptive.Rmd' 'epiR_measures_of_association.Rmd'

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'ggdag'

Package suggested but not available for checking: 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'DT' 'ggplot2' 'knitr' 'pander'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
plot.episplineDensity: no visible global function definition for
  'points'
postproc: no visible global function definition for 'points'
preprocess.data: no visible global function definition for 'sd'
Undefined global functions or variables:
  points sd
Consider adding
  importFrom("graphics", "points")
  importFrom("stats", "sd")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'kableExtra', 'xml2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'roxygen2'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available:
  'emayili', 'rgdal', 'tidyverse', 'xml2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
FCIplot: no visible global function definition for 'na.omit'
FCIplot: no visible global function definition for 'tail'
FCIplot: no visible global function definition for 'grid'
FCIplot: no visible global function definition for 'polygon'
FCIplot: no visible global function definition for 'rgb'
linpred: no visible global function definition for 'lm'
mplott: no visible global function definition for 'par'
mplott: no visible global function definition for 'na.omit'
mplott: no visible global function definition for 'lines'
mplott: no visible global function definition for 'legend'
mplott: no visible global function definition for 'grid'
plott: no visible global function definition for 'lines'
plott: no visible global function definition for 'par'
plott: no visible global function definition for 'grid'
tsideplot: no visible global function definition for 'par'
tsideplot: no visible global function definition for 'axis'
tsideplot: no visible global function definition for 'grid'
Undefined global functions or variables:
  axis grid legend lines lm na.omit par polygon rgb tail
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "axis", "grid", "legend", "lines", "par",
             "polygon")
  importFrom("stats", "lm", "na.omit")
  importFrom("utils", "tail")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'units'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'units'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'TopKLists'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'xml2', 'xslt'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/EPX/EPX.Rcheck/00install.out' for details.
Package required but not available: 'XML'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
eqs2lavaan: no visible global function definition for 'ignore.case'
eqs2lavaan: no visible global function definition for 'str_join'
eqs2lavaan: no visible binding for global variable 'r'
eqsCorr: no visible global function definition for 'cov2cor'
plotCov: no visible global function definition for 'cov2cor'
plotCov: no visible global function definition for 'par'
plotCov: no visible global function definition for 'image'
plotCov: no visible global function definition for 'axis'
Undefined global functions or variables:
  axis cov2cor ignore.case image par r str_join
Consider adding
  importFrom("graphics", "axis", "image", "par")
  importFrom("stats", "cov2cor")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'library' or 'require' call to 'qtl' which was already attached by Depends.
  Please remove these calls from your code.
Unexported objects imported by ':::' calls:
  'qtl:::c.scanone' 'qtl:::plot.scanone'
  See the note in ?`:::` about the use of this operator.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/equalCovs/equalCovs.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/Equalden.HD/Equalden.HD.Rcheck/00install.out' for details.
Package unavailable to check Rd xrefs: 'OpenMx'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'xml2', 'xslt'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/equateMultiple/equateMultiple.Rcheck/00install.out' for details.
The following files contain a license that requires
distribution of original sources:
  'upgreek.sty'
Please ensure that you have complied with it.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'texPreview'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/equivalence/equivalence.Rcheck/00install.out' for details.
Namespaces in Imports field not imported from:
  'cubature' 'rootSolve'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'igraph', 'XML'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'spelling'
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/erboost/erboost.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'btergm'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ergm.count/ergm.count.Rcheck/00install.out' for details.
Package required but not available: 'egor'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ergmito/ergmito.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ergm.rank/ergm.rank.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'latticeExtra'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ergm/ergm.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ergm.userterms/ergm.userterms.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/eRm/eRm.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'signal'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespaces in Imports field not imported from:
  'R6' 'rlang'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'plsVarSel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'parallel'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/errum/errum.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'rasterVis'

Package suggested but not available for checking: 'sf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
ESA: no visible binding for global variable 'var'
plot.esabcv: no visible global function definition for 'points'
plot.esabcv: no visible global function definition for 'axis'
plot.esabcv: no visible global function definition for 'title'
Undefined global functions or variables:
  axis points title var
Consider adding
  importFrom("graphics", "axis", "points", "title")
  importFrom("stats", "var")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/esaddle/esaddle.Rcheck/00install.out' for details.
Package required but not available: 'readODS'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'trialr', 'DiagrammeR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'sf', 'units'

Packages suggested but not available for checking:
  'leafem', 'leaflet', 'tmap'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available:
  'rgdal', 'IRISSeismic', 'XML', 'reticulate'

Package suggested but not available for checking: 'rgl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking:
  'officer', 'rvg', 'hrbrthemes'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Malformed Description field: should contain one or more complete sentences.
cv.ES: no visible binding for global variable 'var'
Undefined global functions or variables:
  var
Consider adding
  importFrom("stats", "var")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/esreg/esreg.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/essentials/essentials.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/essHist/essHist.Rcheck/00install.out' for details.
Package required but not available: 'igraph'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'Hmisc'

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.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/EstHer/EstHer.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'igraph', 'qgraph'

Package suggested but not available for checking: 'JGL'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'vdiffr', 'spelling'
Namespace in Imports field not imported from: 'matrixStats'
  All declared Imports should be used.
Running 'spelling.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(EstimationTools)
  Loading required package: DEoptim
  Loading required package: parallel
  
  DEoptim package
  Differential Evolution algorithm in R
  Authors: D. Ardia, K. Mullen, B. Peterson and J. Ulrich
  
  Loading required package: survival
  Loading required package: stringr
  Loading required package: BBmisc
  
  Attaching package: 'BBmisc'
  
  The following object is masked from 'package:base':
  
      isFALSE
  
  ><<<<<<<<<<<<<<<<<<<<<<<<   EstimationTools Version 2.1.0   >>>>>>>>>>>>>>>>>>>>>>>><
    Feel free to report bugs in https://github.com/Jaimemosg/EstimationTools/issues
  > 
  > test_check("EstimationTools")
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-TTT_HazardShape.R:8:3): plot.HazardShape ────────────────────────
  Error: there is no package called 'vdiffr'
  Backtrace:
      █
   1. └─base::loadNamespace(x) test-TTT_HazardShape.R:8:2
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base:::withOneRestart(expr, restarts[[1L]])
   4.       └─base:::doWithOneRestart(return(expr), restart)
  ── Error (test-TTTplot.R:9:3): plot.empiricalTTT ───────────────────────────────
  Error: there is no package called 'vdiffr'
  Backtrace:
      █
   1. └─base::loadNamespace(x) test-TTTplot.R:9:2
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base:::withOneRestart(expr, restarts[[1L]])
   4.       └─base:::doWithOneRestart(return(expr), restart)
  
  [ FAIL 2 | WARN 0 | SKIP 1 | PASS 18 ]
  Error: Test failures
  Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'modelsummary'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/estimatr/estimatr.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/EstMix/EstMix.Rcheck/00install.out' for details.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'estoutstorage'
descsto: no visible global function definition for 'is'
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
.Transition: no visible global function definition for 'rnorm'
.Transition.DC: no visible global function definition for 'runif'
Simu.Cond.HR: no visible global function definition for 'rpois'
Simu.Cond.HR: no visible global function definition for 'runif'
Simu.Cond.HR: no visible global function definition for 'hist'
Simu.Cond.HR: no visible global function definition for 'var'
Simu.HR: no visible global function definition for 'rpois'
Simu.HR: no visible global function definition for 'runif'
Simu.HR: no visible global function definition for 'hist'
Simu.HR: no visible global function definition for 'var'
Undefined global functions or variables:
  hist rnorm rpois runif var
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "rnorm", "rpois", "runif", "var")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/estudy2/estudy2.Rcheck/00install.out' for details.
Package required but not available: 'Hmisc'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/etasFLP/etasFLP.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ETAS/ETAS.Rcheck/00install.out' for details.
etc.diff: no visible global function definition for 'model.frame'
etc.diff: no visible binding for global variable 'sd'
etc.diff: no visible global function definition for 'qt'
etc.diff: no visible global function definition for 'pt'
etc.diff: no visible global function definition for 'wilcox.test'
etc.rat: no visible global function definition for 'model.frame'
etc.rat: no visible binding for global variable 'sd'
etc.rat: no visible global function definition for 'qt'
etc.rat: no visible global function definition for 'pt'
Undefined global functions or variables:
  model.frame pt qt sd wilcox.test
Consider adding
  importFrom("stats", "model.frame", "pt", "qt", "sd", "wilcox.test")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'rvest', 'xml2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following significant warnings:
  Warning: 'memory.limit()' is no longer supported
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ETLUtils/ETLUtils.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/etm/etm.Rcheck/00install.out' for details.
Package required but not available: 'rvest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'xslt', 'xml2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'spelling'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/eulerr/eulerr.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'RSQLite'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'xml2', 'rvest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'xml2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'RefManageR', 'sf'

Packages suggested but not available for checking:
  'Cairo', 'roxygen2', 'rvest', 'tmap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'mathjaxr'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'shinytest', 'spelling'
Running 'spelling.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(evaluator)
  > 
  > # ensure phantom.js is available on CI platforms
  > if (Sys.getenv("NOT_CRAN", "") != "" || Sys.getenv("CI", "") != "") {
  +   if (!shinytest::dependenciesInstalled()) shinytest:::installDependencies()
  +   message("Using phantom.js from ", shinytest:::find_phantom(), "\n")
  + }
  > 
  > test_check("evaluator")
  # Scenario model: openfair_tef_tc_diff_lm
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • Cannot test dashboard generation without pandoc available. (1)
  • Cannot test report generation without pandoc available. (1)
  • Not running MVA test - EVALUATOR_TEST_MVA not set (1)
  • empty test (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-explore-scenarios.R:4:1): (code run outside of `test_that()`) ───
  Error: there is no package called 'shinytest'
  Backtrace:
      █
   1. └─base::library(shinytest) test-explore-scenarios.R:4:0
  ── Error (test-openfair-example.R:3:1): (code run outside of `test_that()`) ────
  Error: there is no package called 'shinytest'
  Backtrace:
      █
   1. └─base::library(shinytest) test-openfair-example.R:3:0
  
  [ FAIL 2 | WARN 0 | SKIP 4 | PASS 136 ]
  Error: Test failures
  Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'EnvStats'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Malformed Description field: should contain one or more complete sentences.
powerSet : <anonymous>: no visible global function definition for
  'combn'
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/evdbayes/evdbayes.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/evd/evd.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'EventDetectR', 'XML'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/eventglm/eventglm.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/event/event.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespaces in Imports field not imported from:
  'curl' 'openxlsx' 'stringr'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/evgam/evgam.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'rstan', 'rstanarm'

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.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'geiger', 'phytools'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
evolvabilityBetaMCMC : <anonymous>: no visible binding for global
  variable 'median'
evolvabilityBetaMCMC: no visible binding for global variable 'median'
evolvabilityBetaMCMC2: no visible binding for global variable 'median'
evolvabilityMeans: no visible global function definition for 'var'
evolvabilityMeansMCMC : <anonymous>: no visible global function
  definition for 'var'
evolvabilityMeansMCMC: no visible binding for global variable 'median'
randomBeta: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  median rnorm var
Consider adding
  importFrom("stats", "median", "rnorm", "var")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'geomorph'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package in Depends field not imported from: 'evd'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
DPOT: no visible global function definition for 'optim'
mop.rho: no visible global function definition for 'median'
Undefined global functions or variables:
  median optim
Consider adding
  importFrom("stats", "median", "optim")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/evtree/evtree.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/EWGoF/EWGoF.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'parallel'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
EW : PhiP : Phi: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  pnorm
Consider adding
  importFrom("stats", "pnorm")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
BinomialCIone: no visible global function definition for 'na.omit'
PairedCIone: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'sf'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/exactLoglinTest/exactLoglinTest.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ExactMultinom/ExactMultinom.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/exactRankTests/exactRankTests.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'ExactData'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'roxygen2'

Package suggested but not available for checking: 'spelling'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'xml2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'xml2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'png'
Package unavailable to check Rd xrefs: 'png'
Running examples in 'exams-Ex.R' failed
The error most likely occurred in:

> ### Name: nops_eval
> ### Title: Evaluate NOPS Exams
> ### Aliases: nops_eval nops_eval_write
> ### Keywords: utilities
> 
> ### ** Examples
> 
> ## --- Preliminaries ---
> 
> ## load package and enforce par(ask = FALSE)
> library("exams")
> options(device.ask.default = FALSE)
> 
> ## set up a temporary working directory in which all files are managed
> odir <- getwd()
> dir.create(mydir <- tempfile())
> setwd(mydir)
> 
> 
> ## --- Step 1 ---
> ## exam generation
> 
> ## define an exam (= list of exercises)
> myexam <- list(
+   "tstat2.Rnw",
+   "ttest.Rnw",
+   "relfreq.Rnw",
+   "anova.Rnw",
+   c("boxplots.Rnw", "scatterplot.Rnw"),
+   "cholesky.Rnw"
+ )
> 
> ## create multiple exams on the disk with different numbers of points
> ## per exercise (see ?exams2nops for more examples)
> set.seed(403)
> ex1 <- exams2nops(myexam, n = 2, dir = ".", date = "2015-07-29",
+   points = c(1, 1, 1, 2, 2, 3), showpoints = TRUE)
> dir()
[1] "metainfo.rds" "nops1.pdf"    "nops2.pdf"   
> 
> ## assume the PDF exams were already printed (and possibly backed up
> ## in a different directory) so that they are not needed anymore
> file.remove(dir(pattern = "pdf$"))
[1] TRUE TRUE
> 
> 
> ## --- Step 2 ---
> ## scan results
> 
> ## assume two participants filled out the printed exam sheets
> ## and the corresponding scans are in two PNG files,
> img <- dir(system.file("nops", package = "exams"), pattern = "nops_scan",
+   full.names = TRUE)
> 
> ## copy the PNG files to the working directory
> file.copy(img, to = ".")
[1] TRUE TRUE
> 
> ## read the scanned images (all locally available .png files) and collect
> ## results in a ZIP archive (see ?nops_scan for more details)
> nops_scan()
Loading required namespace: png
Failed with error:  'there is no package called 'png''
Error in nops_scan() : requireNamespace("png") is not TRUE
Calls: nops_scan -> stopifnot
Execution halted
Running 'encodings.R'
Running the tests in 'tests/encodings.R' failed.
Complete output:
  > if(!identical(Sys.getlocale(), "C")) {
  + library("exams")
  + exams2pdf("currency8", encoding = "UTF-8",   template = "plain8", dir = ".")
  + exams2pdf("currency9", encoding = "Latin-9", template = "plain9", dir = ".")
  + }
  Loading required namespace: tinytex
  Error: LaTeX failed to compile plain81.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips.
  In addition: Warning message:
  In system2(..., stdout = if (use_file_stdout()) f1 else FALSE, stderr = f2) :
    '"pdflatex"' not found
  Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
plot.pgrid: no visible global function definition for 'image'
statistic.cv: no visible global function definition for 'quantile'
statistic.sim: no visible global function definition for 'contourLines'
Undefined global functions or variables:
  contourLines image quantile
Consider adding
  importFrom("grDevices", "contourLines")
  importFrom("graphics", "image")
  importFrom("stats", "quantile")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/exceedProb/exceedProb.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/excel.link/excel.link.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'reticulate'

Package suggested but not available for checking: 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'INLA', 'rgdal'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/excursions/excursions.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/exdex/exdex.Rcheck/00install.out' for details.
Package required but not available: 'brms'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ExhaustiveSearch/ExhaustiveSearch.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ExomeDepth/ExomeDepth.Rcheck/00install.out' for details.
Namespaces in Imports field not imported from:
  'readr' 'tibble'
  All declared Imports should be used.
Note: found 11 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'gage', 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'kableExtra'

Package suggested but not available for checking: 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'polynom'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'phylobase'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/expectreg/expectreg.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'spelling'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/experiment/experiment.Rcheck/00install.out' for details.
Package required but not available: 'rlist'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
print.cdf : numform: warning in formatC(x, dig = digits): partial
  argument match of 'dig' to 'digits'
print.cdf: warning in get("x", env = environment(x)): partial argument
  match of 'env' to 'envir'
print.cdf: warning in get("y", env = environment(x)): partial argument
  match of 'env' to 'envir'
print.ogive : numform: warning in formatC(x, dig = digits): partial
  argument match of 'dig' to 'digits'
print.ogive: warning in get("x", env = environment(x)): partial
  argument match of 'env' to 'envir'
print.ogive: warning in get("y", env = environment(x)): partial
  argument match of 'env' to 'envir'
quantile.expert: warning in formatC(paste(100 * probs, "%", sep = ""),
  format = "fg", wid = 1, digits = dig): partial argument match of
  'wid' to 'width'
MS: no visible global function definition for 'tail'
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'EBImage'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/expint/expint.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'mediation', 'weights'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking:
  'quanteda', 'quanteda.textmodels'
Package unavailable to check Rd xrefs: 'quanteda.textmodels'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/expm/expm.Rcheck/00install.out' for details.
Namespaces in Imports field not imported from:
  'Matrix' 'RColorBrewer' 'Rcpp' 'e1071' 'foreach' 'gam' 'ggplot2'
  'glmnet' 'nnet' 'polspline' 'repmis' 'splines' 'xgboost'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/expperm/expperm.Rcheck/00install.out' for details.
Package required but not available: 'spdep'

Package suggested but not available for checking: 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/expSBM/expSBM.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'huxtable'
Package unavailable to check Rd xrefs: 'huxtable'
Running examples in 'expss-Ex.R' failed
The error most likely occurred in:

> ### Name: net
> ### Title: Add subtotal to a set of categories
> ### Aliases: net subtotal tab_net_cells tab_net_cols tab_net_rows
> ###   tab_subtotal_cells tab_subtotal_cols tab_subtotal_rows hide unhide
> 
> ### ** Examples
> 
> ol = c(1:7, 99)
> var_lab(ol) = "Liking"
> val_lab(ol)  = num_lab("
+                      1 Disgusting
+                      2 Very Poor
+                      3 Poor
+                      4 So-so
+                      5 Good
+                      6 Very good
+                      7 Excellent
+                      99 Hard to say
+                      ")
>                      
> cro(subtotal(ol, BOTTOM = 1:3, TOP = 6:7, position = "top"))
Error in set_val_lab.default(x, value, add = FALSE) : 
  'set_val_lab' - duplicated values in labels: 1 1 2 2 3 3 4 5 6 6 7 7 99
Calls: cro ... net.default -> val_lab<- -> set_val_lab -> set_val_lab.default
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Malformed Description field: should contain one or more complete sentences.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
index.citations: no visible global function definition for
  'txtProgressBar'
read.exsic: no visible global function definition for 'read.csv'
update.pb: no visible global function definition for
  'setTxtProgressBar'
Undefined global functions or variables:
  read.csv setTxtProgressBar txtProgressBar
Consider adding
  importFrom("utils", "read.csv", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'numDeriv'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package in Depends field not imported from: 'rmeta'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
extfunnel: no visible global function definition for 'qnorm'
extfunnel: no visible global function definition for 'meta.summaries'
extfunnel: no visible global function definition for 'flush.console'
extfunnel: no visible global function definition for 'qt'
extfunnel: no visible global function definition for 'dev.new'
extfunnel: no visible global function definition for 'par'
extfunnel: no visible global function definition for 'polygon'
extfunnel: no visible global function definition for 'segments'
extfunnel: no visible global function definition for 'abline'
extfunnel: no visible global function definition for 'axis'
extfunnel: no visible global function definition for 'box'
Undefined global functions or variables:
  abline axis box dev.new flush.console meta.summaries par polygon
  qnorm qt segments
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "axis", "box", "par", "polygon",
             "segments")
  importFrom("stats", "qnorm", "qt")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
bars: no visible global function definition for 'segments'
cv.binomial: no visible binding for global variable 'var'
cv.binomial: no visible global function definition for 'abline'
cv.normal: no visible binding for global variable 'var'
cv.normal: no visible global function definition for 'abline'
cv.poisson: no visible binding for global variable 'var'
cv.poisson: no visible global function definition for 'abline'
plot.extlasso: no visible global function definition for 'matplot'
plot.extlasso: no visible global function definition for 'axis'
Undefined global functions or variables:
  abline axis matplot segments var
Consider adding
  importFrom("graphics", "abline", "axis", "matplot", "segments")
  importFrom("stats", "var")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
exbio: no visible global function definition for 'as.formula'
exbio: no visible global function definition for 'glm'
exbio: no visible binding for global variable 'gaussian'
exbio: no visible global function definition for 'Gamma'
exbio: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  Gamma as.formula gaussian glm pchisq
Consider adding
  importFrom("stats", "Gamma", "as.formula", "gaussian", "glm", "pchisq")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'rgdal'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/extraDistr/extraDistr.Rcheck/00install.out' for details.
Malformed Description field: should contain one or more complete sentences.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
font_install: no visible global function definition for
  'installed.packages'
font_install: no visible global function definition for
  'install.packages'
fonttable_add: no visible global function definition for 'write.csv'
Undefined global functions or variables:
  install.packages installed.packages write.csv
Consider adding
  importFrom("utils", "install.packages", "installed.packages",
             "write.csv")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
toJavaMatrix2D: no visible global function definition for 'is'
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'sf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'rlist'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/extRemes/extRemes.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/extremis/extremis.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/extWeibQuant/extWeibQuant.Rcheck/00install.out' for details.
Packages suggested but not available for checking: 'exuberdata', 'spelling'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/exuber/exuber.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'dplyr'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Malformed Description field: should contain one or more complete sentences.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'roxygen2'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ezglm/ezglm.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'textreadr', 'mboxr'

Packages suggested but not available for checking: 'xml2', 'rvest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'weights'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
createFormula: no visible global function definition for 'tail'
createFormula: no visible global function definition for 'head'
createFormula: no visible global function definition for 'as.formula'
ezsim: no visible global function definition for 'runif'
plot.ezsim: no visible global function definition for 'quantile'
plot.ezsim: no visible global function definition for 'head'
plot.ezsim: no visible global function definition for 'tail'
plot.ezsim: no visible binding for global variable 'dnorm'
plot.ezsim: no visible binding for global variable 'pdf'
plot.ezsim: no visible global function definition for 'dev.off'
plot.ezsim : <anonymous>: no visible global function definition for
  'dev.new'
plot.summary.ezsim: no visible global function definition for 'head'
plot.summary.ezsim: no visible global function definition for 'tail'
plot.summary.ezsim: no visible binding for global variable 'pdf'
plot.summary.ezsim: no visible global function definition for 'dev.off'
plot.summary.ezsim : <anonymous>: no visible global function definition
  for 'dev.new'
Undefined global functions or variables:
  as.formula dev.new dev.off dnorm head pdf quantile runif tail
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "pdf")
  importFrom("stats", "as.formula", "dnorm", "quantile", "runif")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'rgl'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'spelling'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fable/fable.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'spelling'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fabMix/fabMix.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/facilitation/facilitation.Rcheck/00install.out' for details.
gibbs2: no visible global function definition for 'rnorm'
gibbs_sampling: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Malformed Description field: should contain one or more complete sentences.
fma: no visible global function definition for 'factanal'
fma: no visible global function definition for 'runif'
fma: no visible global function definition for 'kmeans'
fma: no visible global function definition for 'var'
fma.em.alg: no visible global function definition for 'var'
misc : q: no visible global function definition for 'name'
Undefined global functions or variables:
  factanal kmeans name runif var
Consider adding
  importFrom("stats", "factanal", "kmeans", "runif", "var")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/FactoClass/FactoClass.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'igraph'
Package unavailable to check Rd xrefs: 'igraph'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'arm', 'genlasso', 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'survminer'
Namespaces in Imports field not imported from:
  'forcats' 'formula.tools'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'dplyr'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/factorQR/factorQR.Rcheck/00install.out' for details.
Note: found 5 marked Latin-1 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/factorstochvol/factorstochvol.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'roxygen2'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespaces in Imports field not imported from:
  'R6' 'caTools' 'httr' 'jsonlite' 'rlang'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages in Depends field not imported from:
  'RCurl' 'RJSONIO' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
createFactualConnection: no visible global function definition for
  'new'
factualGetSchema: no visible global function definition for 'fromJSON'
factualRead: no visible global function definition for 'curlEscape'
factualRead: no visible global function definition for 'fromJSON'
processFactualReadJSON: no visible global function definition for 'new'
processFactualSchemaJSON: no visible global function definition for
  'new'
Undefined global functions or variables:
  curlEscape fromJSON new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fad/fad.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'stringr'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'optiSolve'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'spelling'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
faisalconjoint: no visible global function definition for 'barplot'
faisalconjoint: no visible global function definition for 'text'
faisalconjoint: no visible global function definition for 'jpeg'
faisalconjoint: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  barplot dev.off jpeg text
Consider adding
  importFrom("grDevices", "dev.off", "jpeg")
  importFrom("graphics", "barplot", "text")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

Packages suggested but not available for checking:
  'devtools', 'lintr', 'packager', 'rasciidoc', 'roxygen2', 'spelling'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/falcon/falcon.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/falconx/falconx.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fame/fame.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/Familias/Familias.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/FamilyRank/FamilyRank.Rcheck/00install.out' for details.
coef.FAMILY: no visible global function definition for 'glm'
coef.FAMILY: no visible global function definition for 'lm'
fm2v: no visible global function definition for 'na.omit'
l_inf_prox: no visible global function definition for 'tail'
predict.FAMILY: no visible global function definition for 'coef'
predict.FAMILY: no visible global function definition for 'lm'
predict.FAMILY: no visible global function definition for 'predict'
predict.FAMILY: no visible global function definition for 'glm'
predict.FAMILY: no visible global function definition for 'predict.glm'
v2fm: no visible global function definition for 'tail'
Undefined global functions or variables:
  coef glm lm na.omit predict predict.glm tail
Consider adding
  importFrom("stats", "coef", "glm", "lm", "na.omit", "predict",
             "predict.glm")
  importFrom("utils", "tail")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/FAmle/FAmle.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages in Depends field not imported from:
  'impute' 'mnormt'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fanc/fanc.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fansi/fansi.Rcheck/00install.out' for details.
Package required but not available: 'XML'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'OpenML'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/farff/farff.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/FarmSelect/FarmSelect.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/FarmTest/FarmTest.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/far/far.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'rlang'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/farver/farver.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'tidyverse'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fAsianOptions/fAsianOptions.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fastAdaboost/fastAdaboost.Rcheck/00install.out' for details.
Packages required but not available: 'reticulate', 'png'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/FastBandChol/FastBandChol.Rcheck/00install.out' for details.
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fastcluster/fastcluster.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fastcmh/fastcmh.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fastcmprsk/fastcmprsk.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fastcox/fastcox.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fastdigest/fastdigest.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'spelling'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fasteraster/fasteraster.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fasterElasticNet/fasterElasticNet.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'sf'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fasterize/fasterize.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/FastGaSP/FastGaSP.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fastGHQuad/fastGHQuad.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fastglm/fastglm.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/FastGP/FastGP.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/FastHCS/FastHCS.Rcheck/00install.out' for details.
basis_hica: no visible global function definition for 'princomp'
energy_hica: no visible global function definition for 'dev.new'
energy_hica: no visible global function definition for 'points'
energy_hica: no visible global function definition for 'legend'
Undefined global functions or variables:
  dev.new legend points princomp
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "legend", "points")
  importFrom("stats", "princomp")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fastICA/fastICA.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fastJT/fastJT.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fastkmedoids/fastkmedoids.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'coxKM'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'spelling'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fastLink/fastLink.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fastlogranktest/fastlogranktest.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/FastLZeroSpikeInference/FastLZeroSpikeInference.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fastmap/fastmap.Rcheck/00install.out' for details.
Package required but not available: 'rgdal'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fastmatch/fastmatch.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fastmatrix/fastmatrix.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fastmit/fastmit.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fastM/fastM.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'igraph', 'tidygraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/FastPCS/FastPCS.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fastpos/fastpos.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'rvest', 'xml2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fastqq/fastqq.Rcheck/00install.out' for details.
Package required but not available: 'mosaic'

Packages suggested but not available for checking:
  'mosaicCalc', 'Hmisc', 'DAAG', 'alr3'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/FastRCS/FastRCS.Rcheck/00install.out' for details.
Packages required but not available: 'igraph', 'tidygraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'Cairo'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/FastSF/FastSF.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'reticulate'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fastshap/fastshap.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fastSOM/fastSOM.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fastText/fastText.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fastTextR/fastTextR.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fasttime/fasttime.Rcheck/00install.out' for details.
Packages suggested but not available for checking:
  'roll', 'stringfish', 'parallelDist', 'qs'
Namespaces in Imports field not imported from:
  'data.table' 'fst' 'kit' 'magrittr' 'matrixStats'
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building 'fastverse_intro.Rmd' using rmarkdown
Quitting from lines 65-73 (fastverse_intro.Rmd) 
Error: processing vignette 'fastverse_intro.Rmd' failed with diagnostics:
there is no package called 'roll'
--- failed re-building 'fastverse_intro.Rmd'

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

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'umap'

Package suggested but not available for checking: 'DESeq2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/FaultTree/FaultTree.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'roxygen2'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'roxygen2', 'kableExtra'
Error(s) in re-building vignettes:
--- re-building 'codebook.Rmd' using rmarkdown

************
Welcome to faux. For support and examples visit:
https://debruine.github.io/faux/
- Get and set global package options with: faux_options()
************
--- finished re-building 'codebook.Rmd'

--- re-building 'continuous.Rmd' using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

--- finished re-building 'continuous.Rmd'

--- re-building 'contrasts.Rmd' using rmarkdown
Quitting from lines 21-58 (contrasts.Rmd) 
Error: processing vignette 'contrasts.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'contrasts.Rmd'

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

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

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

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

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'xml2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'spelling'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fBasics/fBasics.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fbati/fbati.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/FBFsearch/FBFsearch.Rcheck/00install.out' for details.
FBN.histogramMaxima: no visible global function definition for 'hist'
FBN.kmeans: no visible global function definition for 'median'
FBN.kmeans: no visible global function definition for 'kmeans'
FBNormalization: no visible global function definition for 'read.table'
FBNormalization: no visible global function definition for 'median'
FBNormalization: no visible global function definition for 'hist'
FBNormalization: no visible global function definition for 'par'
FBNormalization: no visible global function definition for 'dev.print'
FBNormalization: no visible binding for global variable 'bmp'
FBNormalization: no visible global function definition for 'sd'
FBNormalization: no visible global function definition for
  'write.table'
medianFilter: no visible global function definition for 'median'
Undefined global functions or variables:
  bmp dev.print hist kmeans median par read.table sd write.table
Consider adding
  importFrom("grDevices", "bmp", "dev.print")
  importFrom("graphics", "hist", "par")
  importFrom("stats", "kmeans", "median", "sd")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

Package suggested but not available for checking: 'XML'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fbroc/fbroc.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'tikzDevice'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fcci/fcci.Rcheck/00install.out' for details.
Packages in Depends field not imported from:
  'MASS' 'combinat' 'glmnet'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fcd.cluster: no visible global function definition for 'kmeans'
fcd.start: no visible global function definition for 'ginv'
fcd.start: no visible global function definition for 'glmnet'
gen.dcbm: no visible global function definition for 'rbinom'
gen.sbm: no visible global function definition for 'rbinom'
mis.cluster: no visible global function definition for 'permn'
spectral.clustering: no visible global function definition for 'kmeans'
Undefined global functions or variables:
  ginv glmnet kmeans permn rbinom
Consider adding
  importFrom("stats", "kmeans", "rbinom")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
PTSingleAssetBarrierOption2: no visible global function definition for
  'new'
newton: no visible global function definition for 'abline'
probInRange: no visible global function definition for 'pnorm'
shortfall_risk: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  abline new pnorm
Consider adding
  importFrom("graphics", "abline")
  importFrom("methods", "new")
  importFrom("stats", "pnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fclust/fclust.Rcheck/00install.out' for details.
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking:
  'parallelDist', 'mstknnclust', 'smacof', 'rgl', 'clusterSim'
Packages unavailable to check Rd xrefs: 'clusterSim', 'parallelDist', 'mstknnclust'
Running examples in 'FCPS-Ex.R' failed
The error most likely occurred in:

> ### Name: GenieClustering
> ### Title: Genie Clustering by Gini Index
> ### Aliases: GenieClustering
> ### Keywords: Hierarchical Clustering Agglomerative
> 
> ### ** Examples
> 
> data('Hepta')
> Clust=GenieClustering(Hepta$Data,ClusterNo=7)
Error in GenieClustering(Hepta$Data, ClusterNo = 7) : 
  parallelDist package not loaded or installed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fcros/fcros.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fctbases/fctbases.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'fdapace'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fdaMixed/fdaMixed.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'spelling'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fdaoutlier/fdaoutlier.Rcheck/00install.out' for details.
Package required but not available: 'Hmisc'

Package suggested but not available for checking: 'rgl'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required but not available: 'rgl', 'plot3Drgl'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'tolerance'

Packages suggested but not available for checking: 'plot3Drgl', 'rgl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fda.usc/fda.usc.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fddm/fddm.Rcheck/00install.out' for details.
Namespaces in Imports field not imported from:
  'usethis' 'utils'
  All declared Imports should be used.
Note: found 1 marked Latin-1 string
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Note: found 3 marked Latin-1 strings
  Note: found 3 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'png'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/FD/FD.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'mosaic'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/FDRSeg/FDRSeg.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fdrtool/fdrtool.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/FDX/FDX.Rcheck/00install.out' for details.
Package required but not available: 'rms'

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.
Namespace in Imports field not imported from: 'scales'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/feather/feather.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'png', 'mlr'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'spelling'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/FeatureHashing/FeatureHashing.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'rgl'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespaces in Imports field not imported from:
  'e1071' 'lattice' 'randomForest' 'tibble' 'utils'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'reticulate'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Note: found 20 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fechner/fechner.Rcheck/00install.out' for details.
Packages required but not available:
  'devtools', 'igraph', 'rgdal', 'Hmisc', 'sf', 'xml2'

Package suggested but not available for checking: 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fedmatch/fedmatch.Rcheck/00install.out' for details.
Packages required but not available: 'xml2', 'rvest'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'xml2'

Package suggested but not available for checking: 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespaces in Imports field not imported from:
  'curl' 'prettycode'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/FENmlm/FENmlm.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'rstan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'roxygen2', 'pkgdown'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ffbase/ffbase.Rcheck/00install.out' for details.
Packages required but not available: 'rvest', 'xml2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/FFD/FFD.Rcheck/00install.out' for details.
'library' or 'require' calls in package code:
  'ggplot2' 'gridExtra'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
FFieldPtRepDemo: no visible global function definition for 'ggplot'
FFieldPtRepDemo: no visible binding for global variable 'mtcars'
FFieldPtRepDemo: no visible global function definition for 'aes'
FFieldPtRepDemo: no visible binding for global variable 'mpg'
FFieldPtRepDemo: no visible global function definition for 'geom_point'
FFieldPtRepDemo: no visible global function definition for 'geom_text'
FFieldPtRepDemo: no visible global function definition for 'ggtitle'
FFieldPtRepDemo: no visible global function definition for
  'geom_segment'
FFieldPtRepDemo: no visible global function definition for
  'grid.arrange'
Undefined global functions or variables:
  aes geom_point geom_segment geom_text ggplot ggtitle grid.arrange mpg
  mtcars
Consider adding
  importFrom("datasets", "mtcars")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
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LaTeX errors when creating PDF version.
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Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'roxygen2', 'spelling'
Namespaces in Imports field not imported from:
  'NlcOptim' 'usethis' 'xts'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ff/ff.Rcheck/00install.out' for details.
Package required but not available: 'nflreadr'

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

Package suggested but not available for checking: 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ffstream/ffstream.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fftw/fftw.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fftwtools/fftwtools.Rcheck/00install.out' for details.
ftest: no visible global function definition for 'wilcox.test'
ftest: no visible global function definition for 't.test'
Undefined global functions or variables:
  t.test wilcox.test
Consider adding
  importFrom("stats", "t.test", "wilcox.test")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
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LaTeX errors when creating PDF version.
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Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fGarch/fGarch.Rcheck/00install.out' for details.
Packages required but not available:
  'jpmesh', 'sf', 'stars', 'terra', 'units', 'xml2'

Package suggested but not available for checking: 'roxygen2'

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
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'spelling'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
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Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'kableExtra', 'spelling'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'roxygen2', 'spelling'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'spelling'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'JGL', 'fdapace'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages in Depends field not imported from:
  'mvtnorm' 'numDeriv'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
dmymvnorm: no visible global function definition for 'dmvnorm'
dmymvt: no visible global function definition for 'dmvt'
gof.test: no visible global function definition for 'quantile'
gof.test : ecdf: no visible global function definition for 'mecdf'
gof.test: no visible global function definition for 'jacobian'
gof.test: no visible global function definition for 'var'
gradCdfT: no visible global function definition for 'dt'
gradCdfT: no visible global function definition for 'pt'
gradCdfT: no visible global function definition for 'pmvt'
influFun: no visible global function definition for 'jacobian'
mult.sim: no visible global function definition for 'rnorm'
plackettFormula: no visible global function definition for 'pt'
plackettFormula: no visible global function definition for 'pmvt'
pmymvnorm: no visible global function definition for 'GenzBretz'
pmymvnorm: no visible global function definition for 'TVPACK'
pmymvnorm : <anonymous>: no visible global function definition for
  'pmvnorm'
pmymvt: no visible global function definition for 'GenzBretz'
pmymvt: no visible global function definition for 'TVPACK'
pmymvt : <anonymous>: no visible global function definition for 'pmvt'
rmymvnorm: no visible global function definition for 'rmvnorm'
rmymvt: no visible global function definition for 'rmvt'
Undefined global functions or variables:
  GenzBretz TVPACK dmvnorm dmvt dt jacobian mecdf pmvnorm pmvt pt
  quantile rmvnorm rmvt rnorm var
Consider adding
  importFrom("stats", "dt", "pt", "quantile", "rnorm", "var")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
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Re-running with no redirection of stdout/stderr.
fgeasy: no visible global function definition for 'dist'
fgeasy : cor.est: no visible global function definition for 'cor.test'
fgeasy: no visible binding for global variable 'var'
fgperm : runrand: no visible global function definition for 'runif'
fgperm : runrand: no visible global function definition for 'ave'
fgploc : runrand: no visible global function definition for 'runif'
fgploc : runrand: no visible global function definition for 'ave'
fyshuffle: no visible global function definition for 'runif'
plot.fg: no visible global function definition for 'par'
plot.fg: no visible global function definition for 'segments'
plot.fg: no visible binding for global variable 'quantile'
plot.fg: no visible global function definition for 'abline'
plot.fg: no visible global function definition for 'axis'
summary.fg: no visible binding for global variable 'quantile'
Undefined global functions or variables:
  abline ave axis cor.test dist par quantile runif segments var
Consider adding
  importFrom("graphics", "abline", "axis", "par", "segments")
  importFrom("stats", "ave", "cor.test", "dist", "quantile", "runif",
             "var")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
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Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/FGSG/FGSG.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/FHDI/FHDI.Rcheck/00install.out' for details.
Package required but not available: 'xml2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fHMM/fHMM.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
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Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fICA/fICA.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'numDeriv'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
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Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
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Re-running with no redirection of stdout/stderr.
Package required but not available: 'golem'

Package suggested but not available for checking: 'spelling'

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

Packages suggested but not available for checking:
  'kableExtra', 'imager', 'rgdal', 'RStoolbox'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fields/fields.Rcheck/00install.out' for details.
Package required but not available: 'reqres'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'spelling'
LaTeX errors when creating PDF version.
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Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'phyloseq'
Namespace in Imports field not imported from: 'R6'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
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Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/filearray/filearray.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/filehash/filehash.Rcheck/00install.out' for details.
Malformed Description field: should contain one or more complete sentences.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'filehash' 'DBI'
A package should be listed in only one of these fields.
Packages in Depends field not imported from:
  'RSQLite' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
createSQLite: no visible global function definition for 'dbDriver'
createSQLite: no visible global function definition for 'dbConnect'
createSQLite: no visible global function definition for
  'dbUnloadDriver'
createSQLite: no visible global function definition for 'dbGetQuery'
initializeSQLite: no visible global function definition for 'dbDriver'
initializeSQLite: no visible global function definition for 'dbConnect'
initializeSQLite: no visible global function definition for 'new'
dbDelete,filehashSQLite-character: no visible global function
  definition for 'dbGetQuery'
dbDisconnect,filehashSQLite: no visible global function definition for
  'dbUnloadDriver'
dbFetch,filehashSQLite-character: no visible global function definition
  for 'dbGetQuery'
dbInsert,filehashSQLite-character: no visible global function
  definition for 'dbGetQuery'
dbList,filehashSQLite: no visible global function definition for
  'dbGetQuery'
dbMultiFetch,filehashSQLite-character: no visible global function
  definition for 'dbGetQuery'
Undefined global functions or variables:
  dbConnect dbDriver dbGetQuery dbUnloadDriver new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/filelock/filelock.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
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Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
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Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'spelling'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/filling/filling.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'spelling'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
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Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'rstan', 'survminer'
Package unavailable to check Rd xrefs: 'survminer'
Running examples in 'finalfit-Ex.R' failed
The error most likely occurred in:

> ### Name: surv_plot
> ### Title: Plot survival curves with number-at-risk table
> ### Aliases: surv_plot
> 
> ### ** Examples
> 
> library(finalfit)
> 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

> 
> # Survival plot
> data(colon_s)
> explanatory = c("perfor.factor")
> dependent = "Surv(time, status)"
> colon_s %>%
+   surv_plot(dependent, explanatory, xlab="Time (days)", pval=TRUE, legend="none")
Error in loadNamespace(x) : there is no package called 'survminer'
Calls: %>% ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(finalfit)
  > 
  > test_check("finalfit")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_plots.R:23:2): surv_plot gives plot ─────────────────────────────
  Error: there is no package called 'survminer'
  Backtrace:
      █
   1. ├─testthat::expect_is(...) test_plots.R:23:8
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. ├─finalfit::surv_plot(colon_s, "Surv(time, status)", "age.factor")
   5. │ └─base::do.call(survminer::ggsurvplot, args)
   6. └─base::loadNamespace(x)
   7.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   8.     └─base:::withOneRestart(expr, restarts[[1L]])
   9.       └─base:::doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 10 | SKIP 0 | PASS 130 ]
  Error: Test failures
  Execution halted
LaTeX errors when creating PDF version.
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Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
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Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'XML'
LaTeX errors when creating PDF version.
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Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'readODS'
LaTeX errors when creating PDF version.
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Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'xml2', 'EML'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
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Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
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Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
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Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
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Re-running with no redirection of stdout/stderr.
Packages required but not available: 'arm', 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'reticulate'
LaTeX errors when creating PDF version.
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Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
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Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
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Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
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Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'diveRsity'
Package unavailable to check Rd xrefs: 'diveRsity'
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Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'spelling'
Namespaces in Imports field not imported from:
  'ranger' 'yardstick'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
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Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fingerprint/fingerprint.Rcheck/00install.out' for details.
Packages required but not available: 'Rcmdr', 'rgl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
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Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/finity/finity.Rcheck/00install.out' for details.
Packages required but not available: 'xml2', 'rvest', 'XBRL'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fipp/fipp.Rcheck/00install.out' for details.
Malformed Description field: should contain one or more complete sentences.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespaces in Imports field not imported from:
  'R6' 'jose' 'openssl'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/FiRE/FiRE.Rcheck/00install.out' for details.
Namespaces in Imports field not imported from:
  'knitr' 'rmarkdown'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'dm', 'DiagrammeR'
Error(s) in re-building vignettes:
--- re-building 'Data-Model.Rmd' using rmarkdown
Quitting from lines 18-27 (Data-Model.Rmd) 
Error: processing vignette 'Data-Model.Rmd' failed with diagnostics:
there is no package called 'dm'
--- failed re-building 'Data-Model.Rmd'

--- re-building 'fishdata-examples.Rmd' using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

`summarise()` has grouped output by 'site'. You can override using the `.groups` argument.
--- finished re-building 'fishdata-examples.Rmd'

SUMMARY: processing the following file failed:
  'Data-Model.Rmd'

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
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Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
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Re-running with no redirection of stdout/stderr.
'library' or 'require' call to 'tkrplot' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'methods' 'tkrplot'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
LaTeX errors when creating PDF version.
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Re-running with no redirection of stdout/stderr.
Packages required but not available:
  'RcppParallel', 'rstan', 'rstantools', 'fishualize', 'StanHeaders'

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

Package suggested but not available for checking: 'rgl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 7 marked UTF-8 strings
LaTeX errors when creating PDF version.
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Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
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Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fishMod/fishMod.Rcheck/00install.out' for details.
fishmove : coefs: no visible global function definition for 'coef'
fishmove : coefs: no visible global function definition for 'pf'
fishmove: no visible global function definition for 'lm'
fishmove: no visible global function definition for 'predict.lm'
fishmove.estimate: no visible global function definition for 'quantile'
fishmove.estimate : ddoublenorm: no visible global function definition
  for 'dnorm'
fishmove.query: no visible global function definition for 'hasArg'
fishmove.query : f: no visible global function definition for 'pnorm'
fishmove.query: no visible global function definition for 'uniroot'
pdk: no visible global function definition for 'hasArg'
pdk : eq: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  coef dnorm hasArg lm pf pnorm predict.lm quantile uniroot
Consider adding
  importFrom("methods", "hasArg")
  importFrom("stats", "coef", "dnorm", "lm", "pf", "pnorm", "predict.lm",
             "quantile", "uniroot")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
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Re-running with no redirection of stdout/stderr.
Packages required but not available: 'geiger', 'phytools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
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Re-running with no redirection of stdout/stderr.
Package required but not available: 'respirometry'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'geiger', 'hisse', 'phytools', 'spelling'
Packages unavailable to check Rd xrefs: 'hisse', 'phytools'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
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Re-running with no redirection of stdout/stderr.
Package required but not available: 'png'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/FisPro/FisPro.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/FitARMA/FitARMA.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/FitAR/FitAR.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'spelling'
Namespace in Imports field not imported from: 'jsonlite'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available:
  'varian', 'XML', 'leaflet', 'sf', 'leafgl', 'exactextractr',
  'rayshader', 'OpenImageR'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'Hmisc'
Package unavailable to check Rd xrefs: 'Hmisc'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'devtools'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'XML'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'ihs'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'doMC', 'RSvgDevice'
'library' or 'require' calls in package code:
  'devEMF' 'doMC' 'foreach' 'grDevices'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'rstudioapi'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'rvest', 'xml2'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'fivethirtyeightdata'
Package unavailable to check Rd xrefs: 'fivethirtyeightdata'
Note: found 584 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fixest/fixest.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'pkgdown'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/FKF/FKF.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/FKF.SP/FKF.SP.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/FKSUM/FKSUM.Rcheck/00install.out' for details.
Package required but not available: 'mlr'

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: 'eurostat'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespaces in Imports field not imported from:
  'dplyr' 'evaluate' 'ggplot2'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'paletteer'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/flamingos/flamingos.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/flam/flam.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/flan/flan.Rcheck/00install.out' for details.
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/flars/flars.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/flashClust/flashClust.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespaces in Imports field not imported from:
  'data.table' 'xtable'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'tidyr'
  All declared Imports should be used.
Note: found 82 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'xml2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/flexclust/flexclust.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'Ecdat'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'sf'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/flexrsurv/flexrsurv.Rcheck/00install.out' for details.
Package required but not available: 'spdep'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/flexsurv/flexsurv.Rcheck/00install.out' for details.
Packages required but not available: 'officer', 'xml2', 'gdtools'

Package suggested but not available for checking: 'equatags'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'magrittr'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'rgdal'

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: 'ggsn', 'ggmap', 'rgdal'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'devtools', 'roxygen2'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'tidyverse'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/flipr/flipr.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/FLLat/FLLat.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/float/float.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'spelling'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/flock/flock.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
RIind: no visible global function definition for 'aggregate'
RIind: no visible binding for global variable 'sd'
RIpop: no visible global function definition for 'aggregate'
RIpop: no visible binding for global variable 'sd'
SI: no visible global function definition for 'sd'
SI2: no visible global function definition for 'sd'
SI3: no visible global function definition for 'aggregate'
SI3: no visible global function definition for 'pairs'
SI3: no visible global function definition for 'cor'
SI4: no visible global function definition for 'aggregate'
SI4: no visible global function definition for 'sd'
fCV: no visible global function definition for 'sd'
Undefined global functions or variables:
  aggregate cor pairs sd
Consider adding
  importFrom("graphics", "pairs")
  importFrom("stats", "aggregate", "cor", "sd")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Malformed Title field: should not end in a period.
'library' or 'require' call to 'stats' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
GCV: no visible global function definition for 'lm'
GCV: no visible global function definition for 'resid'
ffplot: no visible global function definition for 'par'
ffplot: no visible global function definition for 'points'
ffplot: no visible global function definition for 'legend'
flowfield: no visible global function definition for 'write.table'
gpr: no visible global function definition for 'quantile'
gpr: no visible global function definition for 'var'
smoothp: no visible global function definition for 'lm'
smoothp: no visible global function definition for 'predict'
smoothp: no visible global function definition for 'resid'
smoothp: no visible global function definition for 'optimize'
Undefined global functions or variables:
  legend lm optimize par points predict quantile resid var write.table
Consider adding
  importFrom("graphics", "legend", "par", "points")
  importFrom("stats", "lm", "optimize", "predict", "quantile", "resid",
             "var")
  importFrom("utils", "write.table")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'nomnoml'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Malformed Description field: should contain one or more complete sentences.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/flsa/flsa.Rcheck/00install.out' for details.
Package required but not available: 'RcppParallel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
export: no visible global function definition for 'write.table'
flux.odae : <anonymous>: no visible global function definition for
  'combn'
mf.flux: no visible global function definition for 'runsd'
plot.fluss: no visible global function definition for 'dev.new'
plot.fluss: no visible global function definition for 'pdf'
plot.fluss: no visible global function definition for 'dev.off'
plot.fluxes: no visible global function definition for 'dev.new'
plot.fluxes: no visible global function definition for 'devAskNewPage'
plot.fluxes: no visible global function definition for 'pdf'
plot.fluxes: no visible global function definition for 'dev.off'
plot.fluxxes: no visible global function definition for 'dev.new'
plot.fluxxes: no visible global function definition for 'devAskNewPage'
plot.fluxxes: no visible global function definition for 'pdf'
plot.fluxxes: no visible global function definition for 'dev.off'
reco.bulk : get.out: no visible global function definition for
  'boxplot.stats'
Undefined global functions or variables:
  boxplot.stats combn dev.new dev.off devAskNewPage pdf runsd
  write.table
Consider adding
  importFrom("grDevices", "boxplot.stats", "dev.new", "dev.off",
             "devAskNewPage", "pdf")
  importFrom("utils", "combn", "write.table")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'kableExtra'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'tidyverse'
Error(s) in re-building vignettes:
--- re-building 'fma-vignette.Rmd' using rmarkdown
Quitting from lines 16-22 (fma-vignette.Rmd) 
Error: processing vignette 'fma-vignette.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'fma-vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/FMCCSD/FMCCSD.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespaces in Imports field not imported from:
  'stats' 'utils'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/FME/FME.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fmerPack/fmerPack.Rcheck/00install.out' for details.
Package required but not available: 'solitude'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'imager'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fmri/fmri.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'ciftiTools'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fMRIscrub/fMRIscrub.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/FMStable/FMStable.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fmtr/fmtr.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/FNN/FNN.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fNonlinear/fNonlinear.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'rvest', 'xml2'

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.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Note: found 41 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Malformed Description field: should contain one or more complete sentences.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'hrbrthemes'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'hrbrthemes'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'igraph', 'ggraph'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Note: found 234 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'devtools'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'footprint.Rmd' using rmarkdown
Quitting from lines 21-25 (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
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fOptions/fOptions.Rcheck/00install.out' for details.
Packages required but not available: 'rvest', 'xml2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'doMC'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'roxygen2'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'dtplyr'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/forecast/forecast.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/forecastSNSTS/forecastSNSTS.Rcheck/00install.out' for details.
Package required but not available: 'imputeTestbench'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/foreign/foreign.Rcheck/00install.out' for details.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' calls to packages already attached by Depends:
  'combinat' 'genetics'
  Please remove these calls from your code.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File 'forensic/R/zzz.R':
  .First.lib calls:
    cat("## Statistical Methods in Forensic Genetics \n")
    cat("## The work was supported by the project 1M06014 of the Ministry of \n        Education, Youth and Sports of the Czech Republic. \n")
    require(genetics, quietly = TRUE)
    require(combinat, quietly = TRUE)

Package startup functions should not change the search path.
Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/forensim/forensim.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/foreSIGHT/foreSIGHT.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/forestControl/forestControl.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'sf', 'blockCV'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'tibble' 'viridis'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'APfun', 'imager'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'reticulate'

Package suggested but not available for checking: 'xml2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
ForImp: no visible global function definition for 'head'
ForImp: no visible global function definition for 'tail'
ForImp: no visible global function definition for 'dist'
medianimp: no visible global function definition for 'quantile'
rancatmat: no visible global function definition for 'runif'
transfmatcat: no visible global function definition for 'qnorm'
transfmatcat: no visible global function definition for 'sd'
Undefined global functions or variables:
  dist head qnorm quantile runif sd tail
Consider adding
  importFrom("stats", "dist", "qnorm", "quantile", "runif", "sd")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Malformed Description field: should contain one or more complete sentences.
INFCvpe: no visible binding for global variable 'INFCstats'
INFCvpe: no visible binding for global variable 'INFCdomain'
Undefined global functions or variables:
  INFCdomain INFCstats
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'meta'
Error(s) in re-building vignettes:
--- re-building 'forplo_vignette.Rmd' using rmarkdown
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  font family not found in Windows font database
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  font family not found in Windows font database
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  font family not found in Windows font database
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  font family not found in Windows font database
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  font family not found in Windows font database
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  font family not found in Windows font database
Quitting from lines 428-476 (forplo_vignette.Rmd) 
Error: processing vignette 'forplo_vignette.Rmd' failed with diagnostics:
there is no package called 'meta'
--- failed re-building 'forplo_vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'lidR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
ForwardSearch.fit: no visible global function definition for 'glm.fit'
ForwardSearch.plot: no visible global function definition for 'lines'
ForwardSearch.pointwise.asymptotics: no visible global function
  definition for 'qnorm'
ForwardSearch.pointwise.asymptotics: no visible global function
  definition for 'dnorm'
Undefined global functions or variables:
  dnorm glm.fit lines qnorm
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "dnorm", "glm.fit", "qnorm")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'TreeSim'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'rgdal'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'foto-vignette.Rmd' using rmarkdown
Quitting from lines 39-52 (foto-vignette.Rmd) 
Error: processing vignette 'foto-vignette.Rmd' failed with diagnostics:
Cannot create RasterLayer object from this file; perhaps you need to install rgdal first
--- failed re-building 'foto-vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fourierin/fourierin.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fourPNO/fourPNO.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Malformed Description field: should contain one or more complete sentences.
GenObs: no visible global function definition for 'rnorm'
GenObs.T: no visible global function definition for 'rt'
MeasL: no visible global function definition for 'rbeta'
OutDet: no visible global function definition for 'median'
RanCur: no visible global function definition for 'rnorm'
init: no visible global function definition for 'prcomp'
Undefined global functions or variables:
  median prcomp rbeta rnorm rt
Consider adding
  importFrom("stats", "median", "prcomp", "rbeta", "rnorm", "rt")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fpeek/fpeek.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fplot/fplot.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fpop/fpop.Rcheck/00install.out' for details.
Package required but not available: 'rneos'

Packages suggested but not available for checking:
  'Rsocp', 'Rnlminb2', 'Rdonlp2', 'dplR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fpow/fpow.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'tidyverse'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespaces in Imports field not imported from:
  'dplyr' 'fable' 'fabletools' 'feasts' 'ggplot2' 'lubridate' 'tibble'
  'tidyr' 'tsibble' 'tsibbledata' 'urca'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fracdiff/fracdiff.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'library' or 'require' calls in package code:
  'pcaPP' 'snowFT' 'wavelets'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
ComputeDCT2FFT: no visible global function definition for 'fft'
ComputeSemipgramFFT: no visible global function definition for 'fft'
WaveVarFD: no visible global function definition for 'modwt'
do.fd.estimate: no visible global function definition for
  'performParallel'
do.fd.estimate2d.simple: no visible global function definition for
  'median'
fd.Genton: no visible global function definition for 'qn'
fd.estimate.matrix: no visible global function definition for
  'performParallel'
fd.plot.legend: no visible global function definition for 'legend'
fd.plot.loglog: no visible global function definition for 'points'
fd.plot.loglog: no visible global function definition for 'abline'
summary.FractalDim: no visible binding for global variable 'sd'
Undefined global functions or variables:
  abline fft legend median modwt performParallel points qn sd
Consider adding
  importFrom("graphics", "abline", "legend", "points")
  importFrom("stats", "fft", "median", "sd")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'imager'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fractional/fractional.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fracture/fracture.Rcheck/00install.out' for details.
Package required but not available: 'netmeta'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/frailtyEM/frailtyEM.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/frailtypack/frailtypack.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/frailtySurv/frailtySurv.Rcheck/00install.out' for details.
Package required but not available: 'lamW'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'utils'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'XML'
Errors in running code in vignettes:
when running code in 'lala2015pmml.Rtex'

> options(prompt = "R> ", continue = "+  ", width = 70, 
+     useFancyQuotes = FALSE)

> r = getOption("repos")

> r["CRAN"] = "http://cran.uk.r-project.org"

> options(repos = r)

> rm(r)

> set.seed(2)

> library(frbs)

> fun <- function(input.xy) {
+     z <- 1/(input.xy[1]^4 + input.xy[2]^4 - 2 * input.xy[1]^2 - 
+         2 * input.xy[2]^2 + 3)
+ }

> input.xy <- expand.grid(seq(-2, 2, 0.14), seq(-2, 
+     2, by = 0.14))

> z <- apply(input.xy, 1, fun)

> data <- cbind(input.xy, z)

> colnames(data) <- c("X", "Y", "Z")

> data <- data[sample(nrow(data)), ]

> cut.indx <- round(0.8 * nrow(data))

> data.tra <- data[1:cut.indx, ]

> data.tst <- data[(cut.indx + 1):nrow(data), 1:2]

> real.val <- data[(cut.indx + 1):nrow(data), 3, drop = FALSE]

> range.data <- apply(data, 2, range)

> method.type <- "WM"

> control <- list(num.labels = 5, type.mf = "GAUSSIAN", 
+     type.defuz = "WAM", type.tnorm = "MIN", type.implication.func = "LUKASIEWICZ", 
+     n .... [TRUNCATED] 

> mod.reg <- frbs.learn(data.tra, range.data, method.type, 
+     control)

> write.frbsPMML(frbsPMML(mod.reg), "modRegress")

  When sourcing 'lala2015pmml.R':
Error: there is no package called 'XML'
Execution halted

  'lala2015frbs.ltx'... OK
  'lala2015pmml.Rtex' using 'UTF-8'... failed
Error(s) in re-building vignettes:
--- re-building 'lala2015frbs.ltx' using tex
texify: C:\jenkins\workspace\miktex\windows\build\source\Libraries\MiKTeX\Core\Utils\Utils.cpp:490: internal error

Warning in system(paste(shQuote(texi2dvi), "--version"), intern = TRUE) :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --version' had status 5
Warning in value[[3L]](cond) : 
--- finished re-building 'lala2015frbs.ltx'

--- re-building 'lala2015pmml.Rtex' using Sweave

Error: processing vignette 'lala2015pmml.Rtex' failed with diagnostics:
 chunk 7 
Error in loadNamespace(x) : there is no package called 'XML'

--- failed re-building 'lala2015pmml.Rtex'

SUMMARY: processing the following file failed:
  'lala2015pmml.Rtex'

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'library' or 'require' calls to packages already attached by Depends:
  'CCP' 'MASS' 'calibrate' 'corpcor'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'CCP' 'MASS' 'calibrate' 'corpcor'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
custom.draw.circle: no visible global function definition for 'lines'
frcc: no visible binding for global variable 'sd'
frcc: no visible global function definition for 'cor.shrink'
frcc: no visible global function definition for 'cor'
frcc: no visible global function definition for 'p.asym'
generate_multivariate_normal_sample: no visible global function
  definition for 'mvrnorm'
plot_units: no visible binding for global variable 'sd'
plot_units: no visible global function definition for 'points'
plot_units: no visible global function definition for 'textxy'
plot_variables: no visible global function definition for 'points'
plot_variables: no visible global function definition for 'textxy'
plot_variables: no visible global function definition for 'segments'
Undefined global functions or variables:
  cor cor.shrink lines mvrnorm p.asym points sd segments textxy
Consider adding
  importFrom("graphics", "lines", "points", "segments")
  importFrom("stats", "cor", "sd")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'fdadensity', 'fdapace'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 1 marked UTF-8 string
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/freealg/freealg.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'smacof'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'xml2'

Packages suggested but not available for checking: 'gifti', 'cifti'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'rgl'
Error(s) in re-building vignettes:
--- re-building 'exploring_included_data.Rmd' using rmarkdown
Loading required package: oro.nifti
oro.nifti 0.11.0
Quitting from lines 14-30 (exploring_included_data.Rmd) 
Error: processing vignette 'exploring_included_data.Rmd' failed with diagnostics:
there is no package called 'rgl'
--- failed re-building 'exploring_included_data.Rmd'

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

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'WGCNA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'rvest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'Hmisc'

Packages suggested but not available for checking: 'mRMRe', 'survminer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'FrF2'

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

Package suggested but not available for checking: 'FrF2.catlg128'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Note: found 50 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'devtools', 'packager'
Package unavailable to check Rd xrefs: 'devtools'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'Hmisc'

Packages suggested but not available for checking:
  'dggrids', 'INLA', 'rgdal', 'spdep'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fRLR/fRLR.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages in Depends field not imported from:
  'Rmpfr' 'partitions'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Bell : nways: no visible global function definition for 'setparts'
Bell: no visible global function definition for 'restrictedparts'
CalIncLapInt : Deriv: no visible global function definition for 'D'
CalIncLapInt: no visible global function definition for 'is.whole'
CalIncLapInt: no visible global function definition for 'mpfr'
CalIncLapInt: no visible global function definition for 'chooseMpfr'
derivErfc : Deriv: no visible global function definition for 'D'
derivErfc : Erfc: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  D chooseMpfr is.whole mpfr pnorm restrictedparts setparts
Consider adding
  importFrom("stats", "D", "pnorm")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fromo/fromo.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/frontier/frontier.Rcheck/00install.out' for details.
Package required but not available: 'rgl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'spelling'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'tidyverse'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'marked', 'pkgdown'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'freesurferformats', 'rgl'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'arm', 'foba', 'Hmisc', 'kknn', 'rrlda'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'reticulate'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking:
  'RTCGA.rnaseq', 'lintr', 'pkgdown'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/FSelectorRcpp/FSelectorRcpp.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespaces in Imports field not imported from:
  'class' 'mlbench' 'neuralnet' 'rpart'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/FSInteract/FSInteract.Rcheck/00install.out' for details.
Packages required but not available:
  'XML', 'googlesheets', 'readtext', 'xml2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'randomForestSRC'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fso/fso.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'spelling'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fs/fs.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'sf', 'lwgeom'

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

Package suggested but not available for checking: 'ggnetwork'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/FSSF/FSSF.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'lintr'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fstcore/fstcore.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'lintr'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fst/fst.Rcheck/00install.out' for details.
Note: found 39 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'flextable'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ftnonpar/ftnonpar.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fts/fts.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fugeR/fugeR.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available:
  'xml2', 'rplos', 'rcrossref', 'aRxiv', 'rentrez'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/FunChisq/FunChisq.Rcheck/00install.out' for details.
Package required but not available: 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'keras', 'tensorflow'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Malformed Description field: should contain one or more complete sentences.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'igraph'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'functiondepends-usage.Rmd' using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 116-137 (functiondepends-usage.Rmd) 
Error: processing vignette 'functiondepends-usage.Rmd' failed with diagnostics:
there is no package called 'igraph'
--- failed re-building 'functiondepends-usage.Rmd'

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

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
.FunFEM.main: no visible global function definition for 'kmeans'
.FunFEM.main: no visible global function definition for 'rmultinom'
.FunFEM.main: no visible global function definition for 'cutree'
.FunFEM.main: no visible global function definition for 'hclust'
.FunFEM.main: no visible global function definition for 'dist'
.FunFEM.main: no visible global function definition for 'par'
.mstep: no visible global function definition for 'cov'
Undefined global functions or variables:
  cov cutree dist hclust kmeans par rmultinom
Consider adding
  importFrom("graphics", "par")
  importFrom("stats", "cov", "cutree", "dist", "hclust", "kmeans",
             "rmultinom")
to your NAMESPACE file.
Note: found 120 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Note: found 1 marked UTF-8 string
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fUnitRoots/fUnitRoots.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'tibble'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'Cairo'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'TDA', 'igraph'

Package suggested but not available for checking: 'Ecdat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'attachment', 'roxygen2'

Package suggested but not available for checking: 'spelling'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fuser/fuser.Rcheck/00install.out' for details.
Namespaces in Imports field not imported from:
  'pROC' 'reshape2' 'survival'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages in Depends field not imported from:
  'RUnit' 'futile.options'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.validateGuardExpression: no visible global function definition for
  'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'leaflet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
fuzzyBHexact: warning in round(pvals, d = dp): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(pprev, d = dp): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(p.minus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(p.plus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(a.minus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(a.plus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(new.p.minus, d = 4): partial argument
  match of 'd' to 'digits'
fuzzyBHexact: warning in round(new.p.plus, d = 4): partial argument
  match of 'd' to 'digits'
fuzzyBHexact: warning in round(pvals, d = 4): partial argument match of
  'd' to 'digits'
fuzzyBHexact: warning in round(pprev, d = 4): partial argument match of
  'd' to 'digits'
fuzzyBHexact: warning in round(tau, d = 4): partial argument match of
  'd' to 'digits'
probRejTies: no visible binding for global variable 'nn'
Undefined global functions or variables:
  nn
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'WGCNA'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'rvest'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fuzzyRankTests/fuzzyRankTests.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'markovchain'
Package unavailable to check Rd xrefs: 'markovchain'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
NeedsCompilation field must take value 'yes' or 'no'
'library' or 'require' call to 'splines' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'splines'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
gensurf: no visible global function definition for 'persp'
gensurf: no visible global function definition for 'rainbow'
plotMF: no visible global function definition for 'plot.new'
plotMF: no visible global function definition for 'plot.window'
plotMF: no visible global function definition for 'runif'
plotMF: no visible global function definition for 'predict'
plotMF: no visible global function definition for 'interpSpline'
plotMF: no visible global function definition for 'lines'
plotMF: no visible global function definition for 'text'
plotMF: no visible global function definition for 'title'
plotMF: no visible global function definition for 'axis'
plotMF: no visible global function definition for 'box'
Undefined global functions or variables:
  axis box interpSpline lines persp plot.new plot.window predict
  rainbow runif text title
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "box", "lines", "persp", "plot.new",
             "plot.window", "text", "title")
  importFrom("stats", "predict", "runif")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'reticulate'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package unavailable to check Rd xrefs: 'cffdrs'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking:
  'spelling', 'modelsummary'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fwildclusterboot/fwildclusterboot.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/fwsim/fwsim.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'JOPS'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'kableExtra'
Error(s) in re-building vignettes:
--- re-building 'chart_themes.Rmd' using rmarkdown
g3viz: visualizing gene/genome/gentics data for fun.
  - Pfam (v33.1)
  - UniProt (date: 2020/08/24)

Any questions, please send emails to <g3viz.group@gmail.com> or post on GitHub <https://github.com/G3viz/g3viz/issues>.
Please send questions to cbioportal@googlegroups.com
--- finished re-building 'chart_themes.Rmd'

--- re-building 'introduction.Rmd' using rmarkdown
Quitting from lines 25-29 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'introduction.Rmd'

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

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'ArrayBin'
crossover: no visible global function definition for 'runif'
exchangeSols: no visible global function definition for 'runif'
fps: no visible global function definition for 'runif'
mutation: no visible global function definition for 'runif'
plotBicluster: no visible global function definition for 'gray'
plotBicluster: no visible global function definition for 'heatmap'
reproduction: no visible global function definition for 'runif'
Undefined global functions or variables:
  gray heatmap runif
Consider adding
  importFrom("grDevices", "gray")
  importFrom("stats", "heatmap", "runif")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gadget2/gadget2.Rcheck/00install.out' for details.
FPTsimul: no visible global function definition for 'runif'
histplot: no visible global function definition for 'dev.new'
histplot: no visible global function definition for 'hist'
histplot: no visible global function definition for 'par'
histplot: no visible global function definition for 'legend'
mdt: no visible binding for global variable 'deltat'
plot.FPTdensity: no visible global function definition for 'dev.new'
res_summary: no visible global function definition for 'write.table'
res_summary: no visible global function definition for 'sd'
res_summary: no visible global function definition for 'median'
vdt: no visible binding for global variable 'deltat'
Undefined global functions or variables:
  deltat dev.new hist legend median par runif sd write.table
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "hist", "legend", "par")
  importFrom("stats", "deltat", "median", "runif", "sd")
  importFrom("utils", "write.table")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available:
  'sf', 'rgdal', 'rosm', 'ggmap', 'ggspatial'

Package suggested but not available for checking: 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gafit/gafit.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'maptools'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
CI.RMSEA: no visible global function definition for 'qchisq'
CI.RMSEA: no visible global function definition for 'pchisq'
GAIPE.RMSEA: no visible global function definition for 'par'
GAIPE.RMSEA: no visible global function definition for 'abline'
GAIPE.RMSEA: no visible global function definition for 'colors'
GAIPE.RMSEA: no visible global function definition for 'text'
GAIPE.RMSEA: no visible global function definition for 'arrows'
GAIPE.RMSEA: no visible global function definition for 'points'
GAIPE.RMSEA: no visible global function definition for 'axis'
GAIPE.RMSEA: no visible global function definition for 'lines'
GAIPE.RMSEA: no visible global function definition for 'legend'
GAIPE.RMSEA: no visible global function definition for 'pchisq'
GAIPE.RMSEA: no visible global function definition for 'qchisq'
GAIPE.RMSEA: no visible global function definition for 'mtext'
GAIPE.RMSEA: no visible global function definition for 'title'
PA.RMSEA: no visible global function definition for 'pchisq'
PA.RMSEA: no visible global function definition for 'qchisq'
Undefined global functions or variables:
  abline arrows axis colors legend lines mtext par pchisq points qchisq
  text title
Consider adding
  importFrom("grDevices", "colors")
  importFrom("graphics", "abline", "arrows", "axis", "legend", "lines",
             "mtext", "par", "points", "text", "title")
  importFrom("stats", "pchisq", "qchisq")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'sf'

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

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

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

Package suggested but not available for checking: 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'hrbrthemes'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'R2BayesX'
Error(s) in re-building vignettes:
--- re-building 'gamboostLSS_Tutorial.Rnw' using Sweave
Loading required package: R2BayesX
Installing package into 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gamboostLSS/gamboostLSS.Rcheck'
(as 'lib' is unspecified)
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


Error: processing vignette 'gamboostLSS_Tutorial.Rnw' failed with diagnostics:
 chunk 11 (label = india_stunting1) 
Error in library("R2BayesX") : there is no package called 'R2BayesX'

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

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

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Malformed Description field: should contain one or more complete sentences.
cvriskMSM: no visible global function definition for 'predict'
plotcvriskMSM: no visible binding for global variable 'lines'
plotcvriskMSM: no visible global function definition for 'lines'
Undefined global functions or variables:
  lines predict
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "predict")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'latticeExtra'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gamesGA/gamesGA.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gamlr/gamlr.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespaces in Imports field not imported from:
  'MASS' 'gamlss'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gamlss.dist/gamlss.dist.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package in Depends field not imported from: 'gamlss'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': 'gamlss:::.gamlss.bi.list'
  See the note in ?`:::` about the use of this operator.
finterp.data.frame: no visible global function definition for
  'as.formula'
finterp.data.frame: no visible global function definition for 'terms'
finterp.data.frame: no visible global function definition for
  'model.matrix'
finterp.data.frame: no visible global function definition for
  'model.frame'
finterp.default: no visible global function definition for 'terms'
finterp.default: no visible global function definition for
  'model.matrix'
finterp.default: no visible global function definition for
  'model.frame'
gamlss.nl: no visible global function definition for 'nlm'
nl: no visible global function definition for 'is'
nlgamlss: no visible global function definition for 'NO'
nlgamlss: no visible global function definition for 'as.gamlss.family'
nlgamlss: no visible global function definition for 'nlm'
nlgamlss: no visible global function definition for 'cov2cor'
summary.nlgamlss: no visible global function definition for 'coef'
summary.nlgamlss: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  NO as.formula as.gamlss.family coef cov2cor is model.frame
  model.matrix nlm pnorm terms
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "as.formula", "coef", "cov2cor", "model.frame",
             "model.matrix", "nlm", "pnorm", "terms")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gamlss/gamlss.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'spdep'
Running examples in 'gamlss.spatial-Ex.R' failed
The error most likely occurred in:

> ### Name: draw.polys
> ### Title: Additional supporting functions for random Markov fields
> ### Aliases: draw.polys polys2nb nb2prec polys2polys nb2nb
> ### Keywords: regression spatial
> 
> ### ** Examples
> 
> # bringing the required libraries
> library(spdep)
Error in library(spdep) : there is no package called 'spdep'
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'vdiffr'
Package unavailable to check Rd xrefs: 'hyperSpec'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gammSlice/gammSlice.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gam/gam.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gamreg/gamreg.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gamsel/gamsel.Rcheck/00install.out' for details.
Packages required but not available: 'rvest', 'XML', 'xml2'

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: 'tensorflow'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'tmap', 'sf'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'spelling'
Namespaces in Imports field not imported from:
  'Rdpack' 'gridExtra' 'utils'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'roxygen2'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gapfill/gapfill.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking:
  'haplo.stats', 'meta', 'rms'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gap/gap.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/GA/GA.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking:
  'tidyverse', 'modeltime', 'roxygen2'
Found the following significant warnings:
  Warning: 'memory.limit()' is no longer supported
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/garchmodels/garchmodels.Rcheck/00install.out' for details.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(garchmodels)
  Loading required package: parsnip
  Loading required package: rugarch
  Loading required package: parallel
  
  Attaching package: 'rugarch'
  
  The following object is masked from 'package:stats':
  
      sigma
  
  Loading required package: rmgarch
  Warning messages:
  1: 'memory.limit()' is no longer supported 
  2: 'memory.limit()' is no longer supported 
  > 
  > library(timetk)
  > library(tidyverse)
  Error in library(tidyverse) : there is no package called 'tidyverse'
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'getting-started.Rmd' using rmarkdown
Loading required package: parsnip
Loading required package: rugarch
Loading required package: parallel

Attaching package: 'rugarch'

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

    sigma

Loading required package: rmgarch
Warning: 'memory.limit()' is no longer supported
Warning: 'memory.limit()' is no longer supported
── Attaching packages ────────────────────────────────────── tidymodels 0.1.3 ──
✔ broom        0.7.9      ✔ rsample      0.1.0 
✔ dials        0.0.10     ✔ tibble       3.1.4 
✔ dplyr        1.0.7      ✔ tidyr        1.1.3 
✔ ggplot2      3.3.5      ✔ tune         0.1.6 
✔ infer        1.0.0      ✔ workflows    0.2.3 
✔ modeldata    0.1.1      ✔ workflowsets 0.1.0 
✔ purrr        0.3.4      ✔ yardstick    0.0.8 
✔ recipes      0.1.16     
── Conflicts ───────────────────────────────────────── tidymodels_conflicts() ──
✖ purrr::discard() masks scales::discard()
✖ dplyr::filter()  masks stats::filter()
✖ dplyr::first()   masks rmgarch::first()
✖ dplyr::lag()     masks stats::lag()
✖ dplyr::last()    masks rmgarch::last()
✖ purrr::reduce()  masks rugarch::reduce()
✖ recipes::step()  masks stats::step()
• Use tidymodels_prefer() to resolve common conflicts.
Quitting from lines 43-47 (getting-started.Rmd) 
Error: processing vignette 'getting-started.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'getting-started.Rmd'

--- re-building 'tuning_univariate_algorithms.Rmd' using rmarkdown
Quitting from lines 43-47 (tuning_univariate_algorithms.Rmd) 
Error: processing vignette 'tuning_univariate_algorithms.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'tuning_univariate_algorithms.Rmd'

SUMMARY: processing the following files failed:
  'getting-started.Rmd' 'tuning_univariate_algorithms.Rmd'

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/garchx/garchx.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'spelling'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'tidyverse'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gaselect/gaselect.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gasper/gasper.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/GaSP/GaSP.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/GAS/GAS.Rcheck/00install.out' for details.
Packages required but not available: 'rstan', 'StanHeaders', 'RcppParallel'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'spelling'
Running 'spelling.R'
Running the tests in 'tests/spelling.R' failed.
Complete output:
  > if(requireNamespace('gateR', quietly = TRUE))
  +   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
  +                              skip_on_cran = TRUE)
  Error in loadNamespace(x) : there is no package called 'spelling'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/GauPro/GauPro.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gausscov/gausscov.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'rgl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'library' or 'require' call to 'orthopolynom' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'orthopolynom' 'polynom'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'jpeg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'simFrame'
contindic.gb2: no visible global function definition for 'contour'
contindic.gb2: no visible global function definition for 'box'
contindic.gb2: no visible global function definition for 'mtext'
contprof.gb2: no visible global function definition for 'image'
contprof.gb2: no visible global function definition for 'heat.colors'
contprof.gb2: no visible global function definition for 'contour'
contprof.gb2: no visible global function definition for 'text'
contprof.gb2: no visible global function definition for 'box'
dplot.cavgb2: no visible global function definition for 'par'
dplot.cavgb2: no visible global function definition for 'curve'
dplot.cavgb2: no visible global function definition for 'legend'
dplot.cavgb2: no visible global function definition for 'lines'
dplot.cgb2: no visible global function definition for 'curve'
dplot.cgb2: no visible global function definition for 'lines'
dplot.cgb2: no visible global function definition for 'legend'
plotsML.gb2: no visible global function definition for 'par'
plotsML.gb2: no visible global function definition for 'abline'
plotsML.gb2: no visible global function definition for 'curve'
plotsML.gb2: no visible global function definition for 'legend'
saveplot : <local>: no visible global function definition for 'dev.set'
saveplot : <local>: no visible global function definition for
  'dev.print'
saveplot : <local>: no visible binding for global variable 'pdf'
Undefined global functions or variables:
  abline box contour curve dev.print dev.set heat.colors image legend
  lines mtext par pdf text
Consider adding
  importFrom("grDevices", "dev.print", "dev.set", "heat.colors", "pdf")
  importFrom("graphics", "abline", "box", "contour", "curve", "image",
             "legend", "lines", "mtext", "par", "text")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gbeta/gbeta.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/GBJ/GBJ.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'rgdal', 'sf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gbm/gbm.Rcheck/00install.out' for details.
Package required but not available: 'rgl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gb/gb.Rcheck/00install.out' for details.
Package in Depends field not imported from: 'tools'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  'tools:::.Rd_get_argument_names' 'tools:::RdTags' 'tools:::fetchRdDB'
  See the note in ?`:::` about the use of this operator.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
coeplot: no visible global function definition for 'axis'
coeplot: no visible global function definition for 'lines'
coeplot: no visible global function definition for 'title'
coeplot: no visible global function definition for 'legend'
corplot: no visible global function definition for 'par'
corplot: no visible global function definition for 'pairs'
corplot: no visible global function definition for 'strwidth'
lm.estimate: no visible global function definition for 'as.formula'
lm.estimate: no visible global function definition for 'glm'
panel.cor: no visible global function definition for 'par'
panel.cor: no visible global function definition for 'cor'
panel.cor: no visible global function definition for 'strwidth'
panel.cor: no visible global function definition for 'text'
panel.smooth.r: no visible global function definition for 'par'
panel.smooth.r: no visible global function definition for 'points'
panel.smooth.r: no visible global function definition for 'lines'
posplot: no visible global function definition for 'par'
posplot: no visible global function definition for 'barplot'
posplot: no visible global function definition for 'points'
Undefined global functions or variables:
  as.formula axis barplot cor glm legend lines pairs par points
  strwidth text title
Consider adding
  importFrom("graphics", "axis", "barplot", "legend", "lines", "pairs",
             "par", "points", "strwidth", "text", "title")
  importFrom("stats", "as.formula", "cor", "glm")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gCat/gCat.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gcdnet/gcdnet.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'paleofire'
Namespace in Imports field not imported from: 'raster'
  All declared Imports should be used.
Note: found 103 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'xml2', 'rvest', 'tm'

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: 'latticeExtra'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gcKrig/gcKrig.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gclm/gclm.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gcmr/gcmr.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/GCPM/GCPM.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/GCSM/GCSM.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'stars', 'sf'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gdalcubes/gdalcubes.Rcheck/00install.out' for details.
Package required but not available: 'sf'

Packages suggested but not available for checking: 'rasterVis', 'gdalUtils'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'WeightedCluster'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'rgdal', 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package in Depends field not imported from: 'tools'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
DownloadGdelt: no visible global function definition for
  'packageVersion'
DownloadGdelt: no visible global function definition for
  'download.file'
GdeltZipToDataframe: no visible global function definition for
  'read.delim'
GdeltZipToDataframe: no visible global function definition for 'unzip'
GetSizeOfGDELT: no visible global function definition for 'read.delim'
IsValidGDELT: no visible global function definition for 'read.delim'
IsValidGDELT: no visible global function definition for 'md5sum'
NormEventCounts: no visible global function definition for
  'download.file'
NormEventCounts: no visible global function definition for 'read.csv'
Undefined global functions or variables:
  download.file md5sum packageVersion read.csv read.delim unzip
Consider adding
  importFrom("utils", "download.file", "packageVersion", "read.csv",
             "read.delim", "unzip")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'leaflet', 'XML', 'rgbif'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'grImport'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/GDINA/GDINA.Rcheck/00install.out' for details.
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gdmp/gdmp.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gdm/gdm.Rcheck/00install.out' for details.
Note: found 1 marked UTF-8 string
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gdpc/gdpc.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'badger'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gdtools/gdtools.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'gdxrrw'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'sf'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gear/gear.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'spelling'
Namespaces in Imports field not imported from:
  'knitr' 'lifecycle'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/GeDS/GeDS.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/GEEaSPU/GEEaSPU.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/geepack/geepack.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gee/gee.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'rootSolve'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/geigen/geigen.Rcheck/00install.out' for details.
Package required but not available: 'phytools'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gelnet/gelnet.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'igraph', 'meta'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'gdistance'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'ggplot2' 'pracma' 'rlang'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Note: found 17 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
plot.rbga: no visible global function definition for 'par'
plot.rbga: no visible global function definition for 'hist'
plot.rbga: no visible global function definition for 'lines'
rbga: no visible global function definition for 'runif'
rbga: no visible global function definition for 'dnorm'
rbga.bin: no visible global function definition for 'dnorm'
rbga.bin: no visible global function definition for 'runif'
Undefined global functions or variables:
  dnorm hist lines par runif
Consider adding
  importFrom("graphics", "hist", "lines", "par")
  importFrom("stats", "dnorm", "runif")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available:
  'ggnetwork', 'ggraph', 'igraph', 'phangorn', 'ShortRead'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
genmvnorm: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'purrr'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'genderdata'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'rgl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'repmis'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'G1DBN', 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'xml2', 'annotate', 'GEOquery'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
t1p1: no visible global function definition for 'var'
t1p1: no visible global function definition for 'pt'
t1p2: no visible global function definition for 'pt'
Undefined global functions or variables:
  pt var
Consider adding
  importFrom("stats", "pt", "var")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'rentrez'

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

Packages suggested but not available for checking: 'DOSE', 'rentrez'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
load.genelist: no visible global function definition for 'read.delim'
Undefined global functions or variables:
  read.delim
Consider adding
  importFrom("utils", "read.delim")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'gRain', 'igraph', 'ggm'

Package suggested but not available for checking: 'RHugin'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/genepi/genepi.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/genepop/genepop.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'rgl', 'png'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/GeneralizedUmatrix/GeneralizedUmatrix.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package in Depends field not imported from: 'parallel'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'shinytest'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/GenEst/GenEst.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'tidyverse'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'GGEBiplots'

Package suggested but not available for checking: 'spelling'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'exactextractr', 'spdep', 'sf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
ForImp.Mahala: no visible global function definition for 'combn'
ForImp.Mahala: no visible global function definition for 'var'
ForImp.Mahala: no visible global function definition for 'quantile'
ForImp.Mahala : <anonymous>: no visible global function definition for
  'var'
ForImp.Mahala : <anonymous> : <anonymous>: no visible global function
  definition for 'var'
ForImp.Mahala : <anonymous> : <anonymous>: no visible global function
  definition for 'quantile'
ForImp.PCA: no visible global function definition for 'cov'
ForImp.PCA: no visible global function definition for 'princomp'
ForImp.PCA: no visible global function definition for 'combn'
ForImp.PCA: no visible global function definition for 'quantile'
ForImp.PCA : <anonymous> : <anonymous>: no visible global function
  definition for 'quantile'
Undefined global functions or variables:
  combn cov princomp quantile var
Consider adding
  importFrom("stats", "cov", "princomp", "quantile", "var")
  importFrom("utils", "combn")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/genieclust/genieclust.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/genie/genie.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/genio/genio.Rcheck/00install.out' for details.
Package required but not available: 'rvest'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/GenKern/GenKern.Rcheck/00install.out' for details.
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/GENLIB/GENLIB.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
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Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Running examples in 'geno2proteo-Ex.R' failed
The error most likely occurred in:

> ### Name: generatingCDSaaFile
> ### Title: Generating a file containing the DNA and AA sequences of all the
> ###   protein coding regions (CDSs) in a genome
> ### Aliases: generatingCDSaaFile
> 
> ### ** Examples
> 
>     # the data folder in this package
>     dataFolder = system.file("extdata", package="geno2proteo") 
> 
>     geneticCodeFile_line = file.path(dataFolder, 
+                                     "geneticCode_standardTable_lines.txt")
>     gtfFile = file.path(dataFolder, 
+                 "Homo_sapiens.GRCh37.74_chromosome16_35Mlong.gtf.gz")
>     DNAfastaFile =  file.path(dataFolder, 
+             "Homo_sapiens.GRCh37.74.dna.chromosome.16.fa_theFirst3p5M.txt.gz")
>     
>     outputFolder = tempdir(); # using the current folder as output folder
>     # calling the function.
>     generatingCDSaaFile(geneticCodeFile_line=geneticCodeFile_line, 
+         gtfFile=gtfFile, DNAfastaFile=DNAfastaFile, outputFolder=outputFolder)
Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  : 
  line 2 did not have 7 elements
Calls: generatingCDSaaFile -> read.table -> scan
Execution halted
Running 'runTests.R'
Running the tests in 'tests/runTests.R' failed.
Complete output:
  > BiocGenerics:::testPackage("geno2proteo")
  Timing stopped at: 1.14 0.09 1.72
  Error in file(file, "rt") : cannot open the connection
  In addition: Warning messages:
  1: In system(command) : '"perl"' not found
  2: In system(command) : '"perl"' not found
  3: In file(file, "rt") :
    cannot open file 'C:\msys64\home\tomas\ucrt3\svn\ucrt3\r_packages\pkgcheck\CRAN\geno2proteo\tmp\Rtmpm6qkX7/Homo_sapiens.GRCh37.74_chromosome16_35Mlong.gtf.gz_AAseq.txt': No such file or directory
  Timing stopped at: 0.12 0 0.18
  Error in file(file, "rt") : cannot open the connection
  In addition: Warning messages:
  1: In system(command) : '"perl"' not found
  2: In file(file, "rt") :
    cannot open file 'C:\msys64\home\tomas\ucrt3\svn\ucrt3\r_packages\pkgcheck\CRAN\geno2proteo\tmp\Rtmpm6qkX7/inputFile_loci_genomicLoc_DNAseq.txt': No such file or directory
  
  
  RUNIT TEST PROTOCOL -- Tue Sep 21 23:14:50 2021 
  *********************************************** 
  Number of test functions: 6 
  Number of errors: 2 
  Number of failures: 0 
  
   
  1 Test Suite : 
  geno2proteo RUnit Tests - 6 test functions, 2 errors, 0 failures
  ERROR in test_generatingCDSaaFile: Error in file(file, "rt") : cannot open the connection
  ERROR in test_genomicLocsToWholeDNASequence: Error in file(file, "rt") : cannot open the connection
  
  Test files with failing tests
  
     test_functionsInGeno2proteo.R 
       test_generatingCDSaaFile 
       test_genomicLocsToWholeDNASequence 
  
  
  Error in BiocGenerics:::testPackage("geno2proteo") : 
    unit tests failed for package geno2proteo
  Execution halted
Errors in running code in vignettes:
when running code in 'geno2proteoIntroduction.Rnw'

> options(width = 72)

> library(geno2proteo)

> dataFolder = system.file("extdata", package = "geno2proteo")

> geneticCodeFile = file.path(dataFolder, "geneticCode_standardTable_lines.txt")

> gtfFile_chr16 = file.path(dataFolder, "Homo_sapiens.GRCh37.74_chromosome16_35Mlong.gtf.gz")

> DNAfastaFile_chr16 = file.path(dataFolder, "Homo_sapiens.GRCh37.74.dna.chromosome.16.fa_theFirst3p5M.txt.gz")

> tmpFolder = tempdir()

> generatingCDSaaFile(geneticCodeFile_line = geneticCodeFile, 
+     gtfFile = gtfFile_chr16, DNAfastaFile = DNAfastaFile_chr16, 
+     outputFolder = .... [TRUNCATED] 

  When sourcing 'geno2proteoIntroduction.R':
Error: line 2 did not have 7 elements
Execution halted

  'geno2proteoIntroduction.Rnw'... failed
Error(s) in re-building vignettes:
--- re-building 'geno2proteoIntroduction.Rnw' using Sweave

Error: processing vignette 'geno2proteoIntroduction.Rnw' failed with diagnostics:
 chunk 3 (label = example_generatingCDSaaFile) 
Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  : 
  line 2 did not have 7 elements

--- failed re-building 'geno2proteoIntroduction.Rnw'

SUMMARY: processing the following file failed:
  'geno2proteoIntroduction.Rnw'

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/genodds/genodds.Rcheck/00install.out' for details.
Package required but not available: 'leaflet'

Package suggested but not available for checking: 'tidyverse'

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

Package suggested but not available for checking: 'junctions'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'SOMbrero'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/GenomicTools/GenomicTools.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'colorspace'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'rgl'
Package unavailable to check Rd xrefs: 'rgl'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/GenSA/GenSA.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'igraph'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/genscore/genscore.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'mvmesh', 'SphericalCubature', 'rgl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/genSurv/genSurv.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gensvm/gensvm.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
splineAnalyze: no visible global function definition for 'var'
splineAnalyze: no visible global function definition for 'par'
splineAnalyze: no visible global function definition for 'lines'
Undefined global functions or variables:
  lines par var
Consider adding
  importFrom("graphics", "lines", "par")
  importFrom("stats", "var")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/geoBayes/geoBayes.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'sf'

Package suggested but not available for checking: 'mapview'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'tibble'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'spdep', 'reldist', 'leaflet', 'rgdal'

Packages suggested but not available for checking:
  'ClustGeo', 'rgl', 'kableExtra', 'sf', 'tmap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'sf'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'terra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
PAEA : <anonymous>: no visible global function definition for
  'integrate'
PAEAAnalysis: no visible global function definition for
  'txtProgressBar'
PAEAAnalysis : <anonymous>: no visible global function definition for
  'setTxtProgressBar'
PAEAAnalysis: no visible global function definition for 'par'
PAEAAnalysis: no visible global function definition for 'barplot'
chdirSig: no visible global function definition for 'prcomp'
chdirSig: no visible global function definition for 'rchisq'
chdirSig: no visible global function definition for 'txtProgressBar'
chdirSig : <anonymous> : <anonymous>: no visible global function
  definition for 'setTxtProgressBar'
chdirplots : <anonymous>: no visible global function definition for
  'par'
chdirplots : <anonymous>: no visible global function definition for
  'arrows'
chdirplots : <anonymous>: no visible global function definition for
  'barplot'
multigmtPAEAAnalysis: no visible global function definition for
  'txtProgressBar'
multigmtPAEAAnalysis : <anonymous>: no visible global function
  definition for 'setTxtProgressBar'
multigmtPAEAAnalysis : <anonymous>: no visible global function
  definition for 'data'
multigmtPAEAAnalysis : <anonymous>: no visible global function
  definition for 'write.table'
Undefined global functions or variables:
  arrows barplot data integrate par prcomp rchisq setTxtProgressBar
  txtProgressBar write.table
Consider adding
  importFrom("graphics", "arrows", "barplot", "par")
  importFrom("stats", "integrate", "prcomp", "rchisq")
  importFrom("utils", "data", "setTxtProgressBar", "txtProgressBar",
             "write.table")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available:
  'rgdal', 'leafpop', 'leaflet', 'mapview'

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

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.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/geodist/geodist.Rcheck/00install.out' for details.
Packages required but not available: 'rgdal', 'sf'

Packages suggested but not available for checking:
  'rasterVis', 'tidyverse', 'ggmap', 'rfigshare'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'rgl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available:
  'rnaturalearth', 'sf', 'imguR', 'geogrid'

Package suggested but not available for checking: 'lintr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'sf', 'xml2'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'rgdal'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/GeoFIS/GeoFIS.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/geoFKF/geoFKF.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'sf'

Package suggested but not available for checking: 'lintr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'rgdal', 'sf'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/geohashTools/geohashTools.Rcheck/00install.out' for details.
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.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'sf'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/geojsonR/geojsonR.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/geojsonsf/geojsonsf.Rcheck/00install.out' for details.
Package required but not available: 'xml2'

Packages suggested but not available for checking:
  'ggmap', 'rasterVis', 'rgdal'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available:
  'nngeo', 'sf', 'tidycensus', 'tigris', 'spdep'

Package suggested but not available for checking: 'redist'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/GEOmap/GEOmap.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'inlmisc', 'spdep'

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

Packages suggested but not available for checking:
  'sf', 'EML', 'emld', 'units', 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/geometries/geometries.Rcheck/00install.out' for details.
Packages required but not available: 'rgdal', 'sf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'spelling', 'rgl'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/geometry/geometry.Rcheck/00install.out' for details.
Package required but not available: 'reticulate'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'geometa', 'XML'

Package suggested but not available for checking: 'roxygen2'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'velociraptr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/geoR/geoR.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'XML'

Package suggested but not available for checking: 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
geoscaleBox: no visible global function definition for 'boxplot'
geoscaleBox: no visible global function definition for 'par'
geoscaleBox: no visible global function definition for 'text'
geoscaleBox: no visible global function definition for 'segments'
geoscaleBox: no visible global function definition for 'rect'
geoscaleBox: no visible global function definition for 'rgb'
geoscaleBox: no visible global function definition for 'polygon'
geoscaleBox: no visible global function definition for 'points'
geoscaleBox: no visible global function definition for 'axis'
geoscalePlot: no visible global function definition for 'par'
geoscalePlot: no visible global function definition for 'text'
geoscalePlot: no visible global function definition for 'segments'
geoscalePlot: no visible global function definition for 'rect'
geoscalePlot: no visible global function definition for 'rgb'
geoscalePlot: no visible global function definition for 'points'
geoscalePlot: no visible global function definition for 'axis'
Undefined global functions or variables:
  axis boxplot par points polygon rect rgb segments text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "axis", "boxplot", "par", "points", "polygon",
             "rect", "segments", "text")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
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:

> ### 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
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'sparklyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/geosphere/geosphere.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'sf'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/geos/geos.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'rgdal'

Package which this enhances but not available for checking: 'INLA'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/geostatsp/geostatsp.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking:
  'DESeq2', 'ChAMP', 'clusterProfiler', 'org.Hs.eg.db'
Error(s) in re-building vignettes:
--- re-building 'GeoTcgaData.Rmd' using rmarkdown
Quitting from lines 283-287 (GeoTcgaData.Rmd) 
Error: processing vignette 'GeoTcgaData.Rmd' failed with diagnostics:
there is no package called 'clusterProfiler'
--- failed re-building 'GeoTcgaData.Rmd'

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

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Malformed Description field: should contain one or more complete sentences.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'rgdal'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following significant warnings:
  Warning: 'memory.limit()' is no longer supported
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/geoTS/geoTS.Rcheck/00install.out' for details.
Namespaces in Imports field not imported from:
  'iterators' 'methods'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'ggspatial', 'sf', 'rgdal'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'roxygen2'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'DiagrammeR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'XML'
Error(s) in re-building vignettes:
--- re-building 'Introduction.Rmd' using rmarkdown_notangle
Quitting from lines 128-153 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
object 'VerHistory' not found
--- failed re-building 'Introduction.Rmd'

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

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'spelling'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gert/gert.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'RSelenium'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gesso/gesso.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
GESTr: no visible global function definition for 'rnorm'
GESTr: no visible global function definition for 'sd'
GESTr : <anonymous>: no visible global function definition for 'pnorm'
TranSAM : magChange: no visible global function definition for 'median'
TranSAM : dstat: no visible global function definition for 'sd'
TranSAM: no visible binding for global variable 'sd'
TranSAM: no visible global function definition for 'quantile'
findReplicateGroups: no visible global function definition for 'qnorm'
findReplicateGroups: no visible global function definition for 'sd'
fitGMM : simulateData: no visible global function definition for
  'rnorm'
fitGMM : simulateData: no visible global function definition for 'sd'
fitGMM: no visible global function definition for 'median'
fitGMM: no visible global function definition for 'ks.test'
fitRockeDurbin: no visible global function definition for 'dist'
fitRockeDurbin : findLowGenes: no visible global function definition
  for 'median'
fitRockeDurbin : findLowGenes: no visible global function definition
  for 'mad'
fitRockeDurbin: no visible binding for global variable 'sd'
getMonotonicConfidences_multiclass: no visible global function
  definition for 'pnorm'
getMonotonicConfidences_multiclass: no visible global function
  definition for 'sd'
Undefined global functions or variables:
  dist ks.test mad median pnorm qnorm quantile rnorm sd
Consider adding
  importFrom("stats", "dist", "ks.test", "mad", "median", "pnorm",
             "qnorm", "quantile", "rnorm", "sd")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespaces in Imports field not imported from:
  'RCurl' 'lubridate' 'readr' 'stats'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'xml2', 'rvest'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'devtools'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'xml2', 'rvest', 'XML'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'xml2'

Package suggested but not available for checking: 'roxygen2'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'xml2'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/getPass/getPass.Rcheck/00install.out' for details.
Namespaces in Imports field not imported from:
  'bitops' 'data.table' 'dplyr' 'httr'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'tidyverse'
Namespaces in Imports field not imported from:
  'scales' 'stringr'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'library' or 'require' call to 'party' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'party'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
gTree: no visible global function definition for 'ctree'
gTree: no visible global function definition for 'ctree_control'
guttmanErrors: no visible global function definition for 'runif'
Undefined global functions or variables:
  ctree ctree_control runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'XML', 'rvest', 'xml2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gettz/gettz.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to 'multtest' which was already attached by Depends.
  Please remove these calls from your code.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'jpeg', 'png'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'rgdal', 'rasterVis'

Package suggested but not available for checking: 'sf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'RGtk2'
Error(s) in re-building vignettes:
--- re-building 'IntroductionToGFD.Rmd' using rmarkdown
Quitting from lines 106-107 (IntroductionToGFD.Rmd) 
Error: processing vignette 'IntroductionToGFD.Rmd' failed with diagnostics:
The GUI cannot be used without packages RGtk2.
--- failed re-building 'IntroductionToGFD.Rmd'

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

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'survminer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'rvest', 'xml2', 'googlesheets'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gfiExtremes/gfiExtremes.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gfilmm/gfilmm.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gfilogisreg/gfilogisreg.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'Hmisc'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gfpop/gfpop.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'vdiffr'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking:
  'Hmisc', 'igraph', 'intergraph', 'roxygen2', 'spelling'
Packages unavailable to check Rd xrefs: 'igraph', 'intergraph'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'plotly'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'transformr'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'spelling'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'scales'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking:
  'lintr', 'spelling', 'vdiffr'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(ggcharts)
  Loading required package: ggplot2
  > 
  > test_check("ggcharts")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-bar_chart.R:8:1): (code run outside of `test_that()`) ───────────
  Error: there is no package called 'vdiffr'
  Backtrace:
      █
   1. └─base::loadNamespace(x) test-bar_chart.R:8:0
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base:::withOneRestart(expr, restarts[[1L]])
   4.       └─base:::doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 4 ]
  Error: Test failures
  Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/GGClassification/GGClassification.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'spelling'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'ggraph', 'igraph', 'tidygraph'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'do', 'set', 'rms', 'base.rms'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'spelling'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking:
  'vdiffr', 'gdtools', 'png', 'pkgdown'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ggdmc/ggdmc.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'vdiffr'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'rgl'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'magrittr'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking:
  'brms', 'rms', 'rstanarm', 'rstantools'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

Package suggested but not available for checking: 'roxygen2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'rgl'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'vdiffr', 'devtools'
Namespaces in Imports field not imported from:
  'R6' 'grDevices' 'scales' 'utils'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'rstan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'vdiffr', 'spelling'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'concaveman', 'units'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ggforce/ggforce.Rcheck/00install.out' for details.
Packages suggested but not available for checking: 'mosaic', 'vdiffr', 'sf'
Package unavailable to check Rd xrefs: 'mosaic'
Running examples in 'ggformula-Ex.R' failed
The error most likely occurred in:

> ### Name: gf_function_2d
> ### Title: Plot functions of two variables
> ### Aliases: gf_function_2d gf_function2d gf_function_contour
> ###   gf_function_tile gf_fun_2d gf_fun2d gf_fun_tile gf_fun_contour
> 
> ### ** Examples
> 
> theme_set(theme_bw())
> gf_function_2d(fun = function(x, y) sin(2 * x * y), xlim = c(-pi, pi), ylim = c(-pi, pi)) %>%
+   gf_refine(scale_fill_viridis_c())
> gf_function_2d(fun = function(x, y) x + y, contour = FALSE)
> gf_function_tile(fun = function(x, y) x * y) %>%
+   gf_function_contour(fun = function(x, y) x * y, color = "white") %>%
+   gf_refine(scale_fill_viridis_c())
> gf_fun_tile(x * y ~ x + y, xlim = c(-3, 3), ylim = c(-2, 2)) %>%
+   gf_fun_contour(x * y ~ x + y, color = "white") %>%
+   gf_refine(scale_fill_viridis_c()) %>%
+   gf_labs(fill = "product")
Error: Problem with `mutate()` column `value`.
ℹ `value = fun(x, y)`.
✖ there is no package called 'mosaic'
Backtrace:
     █
  1. ├─`%>%`(...)
  2. ├─ggformula::gf_labs(., fill = "product")
  3. ├─ggformula::gf_refine(., scale_fill_viridis_c())
  4. │ └─base::Reduce(`+`, list(...), init = object)
  5. ├─ggformula::gf_fun_contour(., x * y ~ x + y, color = "white")
  6. │ └─ggformula::gf_fun_2d(...)
  7. ├─ggformula::gf_fun_tile(...)
  8. │ └─ggformula::gf_fun_2d(...)
  9. │   └─ggformula::gf_function_2d(...)
 10. │     └─`%>%`(...)
 11. ├─dplyr::mutate(., value = fun(x, y))
 12. ├─dplyr:::mutate.data.frame(., value = fun(x, y))
 13. │ └─dplyr:::mutate_cols(.data, ..., caller_env = caller_env())
 14. │   ├─base::withCallingHandlers(...)
 15. │   └─mask$eval_all_mutate(quo)
 16. ├─base::loadNamespace(x)
 17. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
 18. │ │ └─base:::withOneRestart(expr, restarts[[1L]])
 19. │ │   └─base:::doWithOneRestart(return(expr), restart)
 20. │ └─base::stop(cond)
 21. └─(function (e) ...
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'lintr'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'vdiffr', 'spelling'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'vdiffr'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespaces in Imports field not imported from:
  'gridExtra' 'lazyeval' 'readr'
  All declared Imports should be used.
Running examples in 'ggguitar-Ex.R' failed
The error most likely occurred in:

> ### Name: select_chords
> ### Title: Select chords by criteria
> ### Aliases: select_chords
> 
> ### ** Examples
> 
> select_chords(chord_name = 'Major', string_5_fret = 3)
Warning: `filter_()` was deprecated in dplyr 0.7.0.
Please use `filter()` instead.
See vignette('programming') for more help
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Error in if (!is.null(value) && value != "") { : 
  missing value where TRUE/FALSE needed
Calls: select_chords -> narrow_chord
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespaces in Imports field not imported from:
  'grDevices' 'gtable'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'sf', 'vdiffr'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'spelling'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gghilbertstrings/gghilbertstrings.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'tidyverse'
Error(s) in re-building vignettes:
--- re-building 'examples.Rmd' using rmarkdown
Quitting from lines 22-26 (examples.Rmd) 
Error: processing vignette 'examples.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'examples.Rmd'

--- re-building 'ggHoriPlot.Rmd' using rmarkdown
Quitting from lines 29-33 (ggHoriPlot.Rmd) 
Error: processing vignette 'ggHoriPlot.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building 'ggHoriPlot.Rmd'

SUMMARY: processing the following files failed:
  'examples.Rmd' 'ggHoriPlot.Rmd'

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'jpeg', 'png'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'utils'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'sf'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ggip/ggip.Rcheck/00install.out' for details.
Packages suggested but not available for checking: 'ztable', 'moonBook'
Running examples in 'ggiraphExtra-Ex.R' failed
The error most likely occurred in:

> ### Name: ggAncova
> ### Title: Make an interactive plot for an ANCOVA model
> ### Aliases: ggAncova ggAncova.default ggAncova.formula ggAncova.lm
> 
> ### ** Examples
> 
> require(moonBook)
Loading required package: moonBook
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'moonBook'
> require(ggplot2)
Loading required package: ggplot2
> require(ggiraph)
Loading required package: ggiraph
> ggAncova(radial,aes(age,NTAV,color=sex),interactive=TRUE)
Error in ggAncova(radial, aes(age, NTAV, color = sex), interactive = TRUE) : 
  object 'radial' not found
Execution halted
Error(s) in re-building vignettes:
--- re-building 'ggPredict.Rmd' using rmarkdown
Quitting from lines 25-28 (ggPredict.Rmd) 
Error: processing vignette 'ggPredict.Rmd' failed with diagnostics:
object 'radial' not found
--- failed re-building 'ggPredict.Rmd'

--- re-building 'introduction.Rmd' using rmarkdown
Loading required package: ggplot2
Loading required package: ggiraph
Loading required package: ggiraphExtra
Loading required package: TH.data
Loading required package: survival
Loading required package: MASS

Attaching package: 'TH.data'

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

    geyser

Loading required package: moonBook
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'moonBook'
Quitting from lines 58-61 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
object 'acs' not found
--- failed re-building 'introduction.Rmd'

SUMMARY: processing the following files failed:
  'ggPredict.Rmd' 'introduction.Rmd'

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'sf', 'xml2'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ggiraph/ggiraph.Rcheck/00install.out' for details.
Package required but not available: 'unisensR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gglasso/gglasso.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'jpeg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'spelling'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'RgoogleMaps', 'png', 'jpeg'

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

Loading required package: tidyr
Loading required package: ggplot2
--- finished re-building 'using_ggmcmc.Rmd'

--- re-building 'v70i09.Rnw' using knitr
Quitting from lines 62-73 (v70i09.Rnw) 
Error: processing vignette 'v70i09.Rnw' failed with diagnostics:
there is no package called 'Cairo'
--- failed re-building 'v70i09.Rnw'

SUMMARY: processing the following file failed:
  'v70i09.Rnw'

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(ggmix)
  > 
  > test_check("ggmix")
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (10)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-KKT.R:5:1): (code run outside of `test_that()`) ─────────────────
  Error: 'wmic' not found
  Backtrace:
      █
   1. └─ggmix::gen_structured_model(...) test-KKT.R:5:0
   2.   └─popkin::popkin(Xkinship, subpops = subpops, loci_on_cols = TRUE)
   3.     └─popkin::popkin_A(...)
   4.       └─popkin:::solve_m_mem_lim(...)
   5.         └─popkin:::get_mem_lim(factor = mem_factor)
   6.           └─base::system("wmic OS get FreePhysicalMemory /Value", intern = TRUE)
  
  [ FAIL 1 | WARN 0 | SKIP 10 | PASS 0 ]
  Error: Test failures
  Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'qgraph'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/GGMncv/GGMncv.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'qgraph'
Namespaces in Imports field not imported from:
  'Matrix' 'Rdpack'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespaces in Imports field not imported from:
  'productplots' 'scales'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'tidyverse', 'XML'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/GGMselect/GGMselect.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'png', 'tidyverse'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > 
  > 
  > library(testthat)
  > library(ggmulti)
  Loading required package: ggplot2
  > 
  > testthat::test_check("ggmulti")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_generalized_geoms.R:3:1): (code run outside of `test_that()`) ───
  Error: there is no package called 'tidyverse'
  Backtrace:
      █
   1. └─base::library(tidyverse) test_generalized_geoms.R:3:0
  ── Error (test_glyphs.R:2:1): (code run outside of `test_that()`) ──────────────
  Error: there is no package called 'tidyverse'
  Backtrace:
      █
   1. └─base::library(tidyverse) test_glyphs.R:2:0
  ── Error (test_position.R:2:1): (code run outside of `test_that()`) ────────────
  Error: there is no package called 'tidyverse'
  Backtrace:
      █
   1. └─base::library(tidyverse) test_position.R:2:0
  ── Error (test_serialaxes.R:2:1): (code run outside of `test_that()`) ──────────
  Error: there is no package called 'tidyverse'
  Backtrace:
      █
   1. └─base::library(tidyverse) test_serialaxes.R:2:0
  ── Error (test_stat.R:2:1): (code run outside of `test_that()`) ────────────────
  Error: there is no package called 'tidyverse'
  Backtrace:
      █
   1. └─base::library(tidyverse) test_stat.R:2:0
  
  [ FAIL 5 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'vdiffr'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'spelling'
Namespaces in Imports field not imported from:
  'dplyr' 'grid' 'scales'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'roxygen2'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'vdiffr'
Namespace in Imports field not imported from: 'survival'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(ggparty)
  Loading required package: ggplot2
  Loading required package: partykit
  Loading required package: grid
  Loading required package: libcoin
  Loading required package: mvtnorm
  > 
  > test_check("ggparty")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_visuals.R:3:3): plots drawn correctly ───────────────────────────
  Error: there is no package called 'vdiffr'
  Backtrace:
      █
   1. └─base::loadNamespace(x) test_visuals.R:3:2
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base:::withOneRestart(expr, restarts[[1L]])
   4.       └─base:::doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 93 ]
  Error: Test failures
  Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking:
  'Hmisc', 'sf', 'vdiffr', 'xml2'
Namespace in Imports field not imported from: 'mgcv'
  All declared Imports should be used.
Packages unavailable to check Rd xrefs: 'Hmisc', 'sf'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'tidyverse', 'moonBook'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'vdiffr', 'nlmixr'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ggpointdensity/ggpointdensity.Rcheck/00install.out' for details.
Namespaces in Imports field not imported from:
  'dplyr' 'grDevices'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'dplyr'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'Hmisc', 'survminer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'ggmap', 'pkgdown'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'randomForestSRC'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'Cairo', 'png'

Package suggested but not available for checking: 'sf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'devtools'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ggrepel/ggrepel.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'vdiffr'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(ggResidpanel)
  > 
  > test_check("ggResidpanel")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-resid_panel.R:6:1): (code run outside of `test_that()`) ─────────
  Error: there is no package called 'vdiffr'
  Backtrace:
      █
   1. └─base::library(vdiffr) test-resid_panel.R:6:0
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'gRbase'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'vdiffr'
Note: found 6242 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available:
  'do', 'set', 'cutoff', 'rms', 'nomogramFormula'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'ggplot2'
A package should be listed in only one of these fields.
Package in Depends field not imported from: 'ggplot2'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ggroc: no visible global function definition for 'ggplot'
ggroc: no visible global function definition for 'aes'
ggroc: no visible global function definition for 'geom_point'
ggroc: no visible global function definition for 'geom_line'
ggroc: no visible global function definition for 'theme'
ggroc: no visible global function definition for 'element_text'
ggroc: no visible global function definition for 'labs'
ggroc: no visible global function definition for 'ggsave'
Undefined global functions or variables:
  aes element_text geom_line geom_point ggplot ggsave labs theme
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'devtools', 'spelling'
Namespaces in Imports field not imported from:
  'magrittr' 'utils'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'sf'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'vdiffr'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(vdiffr)
  Error in library(vdiffr) : there is no package called 'vdiffr'
  Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'spelling', 'vdiffr'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'sf', 'png', 'ggmap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'pkgdown'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'ggmap'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'devtools'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'sf', 'rosm'

Packages suggested but not available for checking:
  'rgdal', 'stars', 'vdiffr', 'lwgeom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'dplyr' 'tibble'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'Hmisc', 'vdiffr'
Package unavailable to check Rd xrefs: 'Hmisc'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking:
  'metaBMA', 'spelling', 'vdiffr'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'tidyr'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'hexbin'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'gridtext'

Package suggested but not available for checking: 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking:
  'lintr', 'spelling', 'vdiffr'
Note: found 138 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'tikzDevice'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'sf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Skipping vignette re-building
Packages suggested but not available for checking: 'ggmap', 'vdiffr'

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

... incomplete output.  Crash?

  'ggvoronoi.Rmd' using 'UTF-8'... failed to complete the test
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'png'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'ggplot2'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'class'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'refund'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'codemetar'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'R6'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'spelling'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'igraph', 'ggraph'
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
Note: found 11 marked UTF-8 strings
Running examples in 'ghypernet-Ex.R' failed
The error most likely occurred in:

> ### Name: CreateIgGraphs
> ### Title: Convert a list of adjacency matrices to a list of igraph graphs.
> ### Aliases: CreateIgGraphs
> 
> ### ** Examples
> 
> data('adj_karate')
> adj_list <- list(adj_karate)
> glist <- CreateIgGraphs(adj_list, FALSE, FALSE)
Error in loadNamespace(x) : there is no package called 'igraph'
Calls: CreateIgGraphs ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
--- re-building 'Significantlinks.Rmd' using rmarkdown
Quitting from lines 22-28 (Significantlinks.Rmd) 
Error: processing vignette 'Significantlinks.Rmd' failed with diagnostics:
there is no package called 'igraph'
--- failed re-building 'Significantlinks.Rmd'

--- re-building 'Tutorial_NRM.Rmd' using rmarkdown
Quitting from lines 67-71 (Tutorial_NRM.Rmd) 
Error: processing vignette 'Tutorial_NRM.Rmd' failed with diagnostics:
there is no package called 'ggraph'
--- failed re-building 'Tutorial_NRM.Rmd'

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

SUMMARY: processing the following files failed:
  'Significantlinks.Rmd' 'Tutorial_NRM.Rmd'

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/ghyp/ghyp.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
acovamcmc: no visible global function definition for 'rnorm'
acovamcmc: no visible global function definition for 'rgamma'
acovamcmc: no visible binding for global variable 'quantile'
acovamcmc: no visible global function definition for 'quantile'
acovamcmc: no visible global function definition for 'var'
plot.acovamcmc: no visible global function definition for 'dev.new'
plot.acovamcmc: no visible global function definition for 'par'
plot.acovamcmc: no visible global function definition for 'density'
plot.acovamcmc: no visible global function definition for 'acf'
plot.acovamcmc: no visible global function definition for 'contour'
plot.acovamcmc: no visible global function definition for 'image'
plot.acovamcmc: no visible global function definition for 'persp'
Undefined global functions or variables:
  acf contour density dev.new image par persp quantile rgamma rnorm var
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "contour", "image", "par", "persp")
  importFrom("stats", "acf", "density", "quantile", "rgamma", "rnorm",
             "var")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File 'gibbs.met/R/firstlib.R':
  .First.lib calls:
    cat("Naive Gibbs Sampling with Metropolis steps(gibbs.met) loaded\n",     "COPYRIGHT 2008 (c) Longhai Li (http://math.usask.ca/~longhai)\n",     "Type ?begin.gibbs.met for help to this package\n", sep = "")

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.

met_gaussian : one_transition: no visible global function definition
  for 'rnorm'
met_gaussian : one_transition: no visible global function definition
  for 'runif'
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/Gifi/Gifi.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gif/gif.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gifski/gifski.Rcheck/00install.out' for details.
Package required but not available: 'xml2'

Package suggested but not available for checking: 'rgl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'kableExtra'
Error(s) in re-building vignettes:
--- re-building 'GIFTr_tutorial.Rmd' using rmarkdown
Quitting from lines 34-39 (GIFTr_tutorial.Rmd) 
Error: processing vignette 'GIFTr_tutorial.Rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'GIFTr_tutorial.Rmd'

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

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'tibble'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(giftwrap)
  > 
  > test_check("giftwrap")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_giftwrap.R:4:3): giftwrap captures output ───────────────────────
  Error: Command 'echo' not found @win/processx.c:982 (processx_exec)
  Backtrace:
       █
    1. ├─testthat::expect_equal(...) test_giftwrap.R:4:2
    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─giftwrap:::giftwrap("echo hey", process_echo = F)
    5. │ └─processx::run(...)
    6. │   └─process$new(...)
    7. │     └─processx:::initialize(...)
    8. │       └─processx:::process_initialize(...)
    9. │         └─rethrow_call(...)
   10. │           ├─base::withCallingHandlers(...)
   11. │           └─base::do.call(".Call", list(.NAME, ...))
   12. └─base::.handleSimpleError(...)
   13.   └─h(simpleError(msg, call))
   14.     └─throw(e)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 66 ]
  Error: Test failures
  Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gigg/gigg.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/GIGrvg/GIGrvg.Rcheck/00install.out' for details.
Package required but not available: 'dynutils'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'igraph', 'qgraph', 'imputeTS'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'EBImage', 'png'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/GiniDistance/GiniDistance.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'rgdal'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/GiRaF/GiRaF.Rcheck/00install.out' for details.
Packages required but not available: 'sf', 'lwgeom'

Package suggested but not available for checking: 'tmap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
choro.legend: no visible global function definition for 'strwidth'
choro.legend: no visible global function definition for 'legend'
choro.legend: no visible global function definition for 'text'
jitter.points: no visible global function definition for 'rnorm'
level.plot: no visible global function definition for '.filled.contour'
map.scale: no visible global function definition for 'par'
map.scale: no visible global function definition for 'rect'
map.scale: no visible global function definition for 'lines'
map.scale: no visible global function definition for 'text'
map.scale: no visible global function definition for 'strheight'
north.arrow: no visible global function definition for 'polygon'
north.arrow: no visible global function definition for 'text'
north.arrow: no visible global function definition for 'strheight'
poly.labels: no visible global function definition for 'slot'
poly.labels : <anonymous>: no visible global function definition for
  'slot'
quantileCuts: no visible global function definition for 'quantile'
sdCuts: no visible global function definition for 'sd'
Undefined global functions or variables:
  .filled.contour legend lines par polygon quantile rect rnorm sd slot
  strheight strwidth text
Consider adding
  importFrom("graphics", ".filled.contour", "legend", "lines", "par",
             "polygon", "rect", "strheight", "strwidth", "text")
  importFrom("methods", "slot")
  importFrom("stats", "quantile", "rnorm", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'spelling'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/git2r/git2r.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespaces in Imports field not imported from:
  'Rcpp' 'mockery'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'shinyFiles'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
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'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'spelling'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gjam/gjam.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'matrixcalc'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking:
  'rtracklayer', 'BSgenome', 'BSgenome.Hsapiens.UCSC.hg18.masked',
  'BSgenome.Hsapiens.UCSC.hg19.masked'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gkmSVM/gkmSVM.Rcheck/00install.out' for details.
Package required but not available: 'Ecdat'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/glamlasso/glamlasso.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'spelling'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'doMC'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/glassoFast/glassoFast.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/glasso/glasso.Rcheck/00install.out' for details.
fptcdf: no visible global function definition for 'dnorm'
fptcdf: no visible global function definition for 'pnorm'
fptpdf: no visible global function definition for 'pnorm'
fptpdf: no visible global function definition for 'dnorm'
lba: no visible global function definition for 'as.formula'
lba: no visible global function definition for 'model.frame'
lba : logl: no visible global function definition for 'head'
lba: no visible global function definition for 'optim'
pmod: no visible global function definition for 'model.frame'
pmod: no visible global function definition for 'model.matrix'
rlba: no visible global function definition for 'pnorm'
rlba: no visible global function definition for 'rnorm'
rlba: no visible global function definition for 'runif'
tablba: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  as.formula dnorm head model.frame model.matrix optim pnorm rnorm
  runif
Consider adding
  importFrom("stats", "as.formula", "dnorm", "model.frame",
             "model.matrix", "optim", "pnorm", "rnorm", "runif")
  importFrom("utils", "head")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/glca/glca.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/glcm/glcm.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/GLDEX/GLDEX.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gld/gld.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/GLIDE/GLIDE.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/glinternet/glinternet.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gllm/gllm.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gllvm/gllvm.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/GLMaSPU/GLMaSPU.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/GLMcat/GLMcat.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/glm.deploy/glm.deploy.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/glmdisc/glmdisc.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/glmlep/glmlep.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'pkgdown'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/glmmEP/glmmEP.Rcheck/00install.out' for details.
Packages required but not available: 'rstan', 'rstantools', 'StanHeaders'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/glmmML/glmmML.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/glmm/glmm.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'kableExtra'
Error(s) in re-building vignettes:
--- re-building 'glmmSeq.rmd' using rmarkdown
Quitting from lines 21-24 (glmmSeq.rmd) 
Error: processing vignette 'glmmSeq.rmd' failed with diagnostics:
there is no package called 'kableExtra'
--- failed re-building 'glmmSeq.rmd'

SUMMARY: processing the following file failed:
  'glmmSeq.rmd'

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/glmmsr/glmmsr.Rcheck/00install.out' for details.
Packages suggested but not available for checking: 'png', 'huxtable'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/glmmTMB/glmmTMB.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/glmnet/glmnet.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespaces in Imports field not imported from:
  'AER' 'MASS' 'Matrix' 'censReg' 'effects' 'foreign' 'lme4' 'lmtest'
  'nnet' 'pBrackets' 'plm' 'pscl' 'sandwich'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/glmpath/glmpath.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'devtools'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'purrr'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Malformed Description field: should contain one or more complete sentences.
.nPerms: no visible global function definition for 'terms'
expr.dev.test: no visible global function definition for 'terms'
expr.dev.test: no visible global function definition for 'model.matrix'
expr.dev.test: no visible global function definition for 'pchisq'
lancaster: no visible global function definition for 'pgamma'
liptak: no visible global function definition for 'pnorm'
summary.dev.test : ci: no visible global function definition for
  'qnorm'
varwiselogLik : <anonymous>: no visible global function definition for
  'deviance'
varwiselogLik.regression: no visible global function definition for
  'glm.fit'
Undefined global functions or variables:
  deviance glm.fit model.matrix pchisq pgamma pnorm qnorm terms
Consider adding
  importFrom("stats", "deviance", "glm.fit", "model.matrix", "pchisq",
             "pgamma", "pnorm", "qnorm", "terms")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'cplexAPI'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Malformed Title field: should not end in a period.
CreateFormula: no visible global function definition for 'as.formula'
GeneratePvalues: no visible binding for global variable 'binomial'
globalARTP: no visible binding for global variable 'binomial'
globalFisher: no visible binding for global variable 'binomial'
globalFisher: no visible global function definition for 'pchisq'
globalSimes: no visible binding for global variable 'binomial'
pvalFmla: no visible binding for global variable 'binomial'
pvalFmla: no visible global function definition for 'glm'
pvalFmla: no visible global function definition for 'anova'
runPermut: no visible binding for global variable 'binomial'
runPvalues: no visible binding for global variable 'binomial'
Undefined global functions or variables:
  anova as.formula binomial glm pchisq
Consider adding
  importFrom("stats", "anova", "as.formula", "binomial", "glm", "pchisq")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/globalKinhom/globalKinhom.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/globalOptTests/globalOptTests.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'RcppParallel'

Package suggested but not available for checking: 'qs'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/glpkAPI/glpkAPI.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Malformed Description field: should contain one or more complete sentences.
ScoreTest: no visible global function definition for 'pchisq'
Var1: no visible global function definition for 'runif'
gLRT1: no visible global function definition for 'pchisq'
gLRT2: no visible global function definition for 'pchisq'
gLRT3: no visible global function definition for 'pchisq'
gLRT4: no visible global function definition for 'pf'
Undefined global functions or variables:
  pchisq pf runif
Consider adding
  importFrom("stats", "pchisq", "pf", "runif")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'mvSLOUCH'
Package unavailable to check Rd xrefs: 'mvSLOUCH'
Running examples in 'GLSME-Ex.R' failed
The error most likely occurred in:

> ### Name: GLSME-package
> ### Title: Generalized Least Squares with Measurement Error
> ### Aliases: GLSME-package
> ### Keywords: generalized least squares regression measurement error
> 
> ### ** Examples
> 
> n<-3 ## number of species
> apetree<-ape::rtree(n)
> ### Define Brownian motion parameters to be able to simulate data under the Brownian motion model.
> BMparameters<-list(vX0=matrix(0,nrow=2,ncol=1),Sxx=rbind(c(1,0),c(0.2,1)))
> ### Now simulate the data and remove the values corresponding to the internal nodes.
> xydata<-mvSLOUCH::simulBMProcPhylTree(apetree,X0=BMparameters$vX0,Sigma=BMparameters$Sxx)
Error in loadNamespace(x) : there is no package called 'mvSLOUCH'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking:
  'rvest', 'spelling', 'xml2'
Error(s) in re-building vignettes:
--- re-building 'github-spec.Rmd' using rmarkdown
Quitting from lines 21-24 (github-spec.Rmd) 
Error: processing vignette 'github-spec.Rmd' failed with diagnostics:
there is no package called 'rvest'
--- failed re-building 'github-spec.Rmd'

--- re-building 'literal-programming.Rmd' using rmarkdown
Quitting from lines 20-24 (literal-programming.Rmd) 
Error: processing vignette 'literal-programming.Rmd' failed with diagnostics:
there is no package called 'rvest'
--- failed re-building 'literal-programming.Rmd'

SUMMARY: processing the following files failed:
  'github-spec.Rmd' 'literal-programming.Rmd'

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/glue/glue.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'xml2'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'Hmisc', 'RcmdrMisc', 'rgdal'

Package suggested but not available for checking: 'gdistance'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'gRbase', 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'Hmisc', 'jpeg'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/GMCM/GMCM.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gMCP/gMCP.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/Gmedian/Gmedian.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gmeta/gmeta.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gmGeostats/gmGeostats.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'Hmisc', 'XML'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'doMC'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/GMMAT/GMMAT.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gmm/gmm.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package unavailable to check Rd xrefs: 'rms'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'rgl', 'png'

Packages suggested but not available for checking:
  'tikzDevice', 'roxygen2', 'tidyverse', 'webshot2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gmp/gmp.Rcheck/00install.out' for details.
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/GMSE/GMSE.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'qgraph'
Package unavailable to check Rd xrefs: 'qgraph'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gMWT/gMWT.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/GNE/GNE.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gnlm/gnlm.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gnm/gnm.Rcheck/00install.out' for details.
Packages required but not available: 'keras', 'tensorflow'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'XML'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'yarrr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/goffda/goffda.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/GofKmt/GofKmt.Rcheck/00install.out' for details.
Namespaces in Imports field not imported from:
  'rhandsontable' 'shiny' 'stats'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/goftest/goftest.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'WGCNA'

Package suggested but not available for checking: 'WGCNA'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
Packages in Depends field not imported from:
  'fGarch' 'fastICA'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
UprodR: no visible global function definition for 'combn'
goinit: no visible global function definition for 'as.formula'
ccor,GoGARCH : <anonymous>: no visible global function definition for
  'cov2cor'
ccor,Gopredict : <anonymous>: no visible global function definition for
  'cov2cor'
goest,Goestica: no visible global function definition for 'fastICA'
goest,Goestml: no visible global function definition for 'nlminb'
goest,Goestmm : <anonymous>: no visible global function definition for
  'combn'
goest,Goestnls: no visible global function definition for 'optim'
show,Goinit: no visible global function definition for 'head'
show,Gopredict: no visible global function definition for 'head'
update,GoGARCH: no visible global function definition for
  'update.formula'
update,Goestica: no visible global function definition for
  'update.formula'
update,Goestml: no visible global function definition for
  'update.formula'
update,Goestmm: no visible global function definition for
  'update.formula'
update,Goestnls: no visible global function definition for
  'update.formula'
Undefined global functions or variables:
  as.formula combn cov2cor fastICA head nlminb optim update.formula
Consider adding
  importFrom("stats", "as.formula", "cov2cor", "nlminb", "optim",
             "update.formula")
  importFrom("utils", "combn", "head")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'tm'

Package suggested but not available for checking: 'RISmed'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'lintr', 'xml2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'ganalytics'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'devtools', 'roxygen2'
Package unavailable to check Rd xrefs: 'devtools'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages unavailable to check Rd xrefs: 'devtools', 'pkgdown'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'roxygen2', 'spelling'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'rvest', 'xml2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'rvest', 'xml2'
'LazyData' is specified without a 'data' directory
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(googleLanguageR)
  > 
  > test_check("googleLanguageR")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_gl.R:1:1): (code run outside of `test_that()`) ──────────────────
  Error: there is no package called 'rvest'
  Backtrace:
      █
   1. ├─base::source("prep_tests.R") test_gl.R:1:0
   2. │ ├─base::withVisible(eval(ei, envir))
   3. │ └─base::eval(ei, envir)
   4. │   └─base::eval(ei, envir)
   5. └─base::library(rvest)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'sf'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/googlePolylines/googlePolylines.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'XML'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'spelling'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'xml2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'assertthat' 'future' 'httr' 'jsonlite'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'jpeg'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'reticulate'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Malformed Description field: should contain one or more complete sentences.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gower/gower.Rcheck/00install.out' for details.
Packages required but not available:
  'GO.db', 'ggraph', 'igraph', 'biomaRt', 'annotate'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'rgl'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Random.Start: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/GPBayes/GPBayes.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gpboost/gpboost.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gpclib/gpclib.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/GPCMlasso/GPCMlasso.Rcheck/00install.out' for details.
.r1: no visible global function definition for 'cor'
.r2: no visible global function definition for 'cor'
rgp: no visible global function definition for 'runif'
rgp: no visible global function definition for 'rexp'
Undefined global functions or variables:
  cor rexp runif
Consider adding
  importFrom("stats", "cor", "rexp", "runif")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/GPFDA/GPFDA.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/GpGp/GpGp.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gpg/gpg.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'dplyr'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gplite/gplite.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gplm/gplm.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/GPM/GPM.Rcheck/00install.out' for details.
Package required but not available: 'GPoM'

Package suggested but not available for checking: 'rgl'

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

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

Package suggested but not available for checking: 'roxygen2'

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.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'rstan'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'nbpMatching'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/GPvam/GPvam.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/GPvecchia/GPvecchia.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'roxygen2'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Malformed Title field: should not end in a period.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'sf'

Package suggested but not available for checking: 'rgdal'

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

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

Package suggested but not available for checking: 'spelling'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'hexSticker'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'rgl'
'library' or 'require' calls in package code:
  'mgcv' 'rgl' 'tcltk'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Running examples in 'granova-Ex.R' failed
The error most likely occurred in:

> ### Name: granova.2w
> ### Title: Graphical display of data for two-way analysis of variance
> ### Aliases: granova.2w
> ### Keywords: hplot
> 
> ### ** Examples
> 
>  
> # using the R dataset warpbreaks; see documentation 
> #(first surface flat since fit = 'linear' (default); 
> #second surface shows curvature)
> granova.2w(warpbreaks)
Loading required package: rgl
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'rgl'
Loading required package: tcltk
Loading required package: mgcv
Loading required package: nlme
This is mgcv 1.8-36. For overview type 'help("mgcv-package")'.
[1] breaks ~ wool * tension
Loading required namespace: rgl
Failed with error:  'there is no package called 'rgl''
Error in scatter3d(facA.mn.cntrst, yy, facB.mn.cntrst, xlab = colnames(data.A.B)[2],  : 
  rgl package missing
Calls: granova.2w -> scatter3d
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'kableExtra', 'Hmisc'

Package suggested but not available for checking: 'shinytest'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available:
  'adegenet', 'igraph', 'pegas', 'sf', 'diveRsity', 'gdistance'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'reshape2'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'sparklyr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'sf'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

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

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

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

Package suggested but not available for checking: 'ggraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'igraph'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/graphql/graphql.Rcheck/00install.out' for details.
Package required but not available: 'rgl'

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

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: 'Matrix'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
GrassmannOptim: no visible global function definition for 'rnorm'
GrassmannOptim: no visible global function definition for 'runif'
GrassmannOptim : <anonymous>: no visible global function definition for
  'expm'
GrassmannOptim : <anonymous>: no visible global function definition for
  'Matrix'
Undefined global functions or variables:
  Matrix expm rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'vdiffr'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'quadmesh'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking:
  'rsdmx', 'taxstats', 'taxstats1516'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/grattan/grattan.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'igraph'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'gRbase'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'igraph', 'spelling'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/greed/greed.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/GreedyEPL/GreedyEPL.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'nbpMatching'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/greeks/greeks.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'Gmisc', 'Hmisc', 'rms'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gremlin/gremlin.Rcheck/00install.out' for details.
Package required but not available: 'igraph'

Package suggested but not available for checking: 'spelling'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gren/gren.Rcheck/00install.out' for details.
Packages required but not available: 'Hmisc', 'rms', 'latticeExtra'

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

Packages suggested but not available for checking:
  'DiagrammeR', 'tidyverse', 'spelling'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gretel/gretel.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'lamW'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'DiagrammeR'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/grf/grf.Rcheck/00install.out' for details.
Malformed Description field: should contain one or more complete sentences.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'gridSVG'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'gridSVG'
grid.graph: no visible global function definition for 'is'
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/GridOnClusters/GridOnClusters.Rcheck/00install.out' for details.
Packages required but not available: 'png', 'sf'

Package suggested but not available for checking: 'vdiffr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'BiasedUrn'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'XML'

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

Package suggested but not available for checking: 'vdiffr'

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

Package suggested but not available for checking: 'gridSVG'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'usethis'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'spelling'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'msm'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'png'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/groc/groc.Rcheck/00install.out' for details.
Package required but not available: 'igraph'

Package suggested but not available for checking: 'phangorn'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'rlist'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'snplist'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/groupedSurv/groupedSurv.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/groupRemMap/groupRemMap.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/groupsubsetselection/groupsubsetselection.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespaces in Imports field not imported from:
  'MASS' 'rjags'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/grove/grove.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/growfunctions/growfunctions.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Malformed Description field: should contain one or more complete sentences.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/growthrates/growthrates.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/growth/growth.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/grpCox/grpCox.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/grpreg/grpreg.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/grpsel/grpsel.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/grpSLOPE/grpSLOPE.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'Rcpp'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespace in Imports field not imported from: 'MASS'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/grr/grr.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'rgl'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
PCgamma : <anonymous>: no visible global function definition for
  'prcomp'
PCgamma : <anonymous> : <anonymous>: no visible global function
  definition for 'glm'
PCgamma : <anonymous> : <anonymous>: no visible global function
  definition for 'update'
PCgamma : <anonymous> : <anonymous>: no visible global function
  definition for 'pchisq'
PCgamma : <anonymous> : <anonymous>: no visible global function
  definition for 'lm'
PCgamma : <anonymous> : <anonymous>: no visible global function
  definition for 'anova'
PCgamma: no visible global function definition for 'qgamma'
PCgamma: no visible global function definition for 'pgamma'
RNAgamma : rnafunc: no visible global function definition for
  'model.matrix'
RNAgamma : rnafunc: no visible global function definition for
  'as.formula'
RNAgamma: no visible global function definition for 'qgamma'
RNAgamma: no visible global function definition for 'pgamma'
STTtoShapeParameter : f: no visible global function definition for
  'qgamma'
STTtoShapeParameter: no visible global function definition for
  'optimize'
Undefined global functions or variables:
  anova as.formula glm lm model.matrix optimize pchisq pgamma prcomp
  qgamma update
Consider adding
  importFrom("stats", "anova", "as.formula", "glm", "lm", "model.matrix",
             "optimize", "pchisq", "pgamma", "prcomp", "qgamma",
             "update")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
.gsa.assignGATKTableToEnvironment: no visible global function
  definition for 'type.convert'
Undefined global functions or variables:
  type.convert
Consider adding
  importFrom("utils", "type.convert")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'library' or 'require' call to 'impute' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
GSA: no visible global function definition for 'impute.knn'
Undefined global functions or variables:
  impute.knn
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'igraph', 'missSBM'
Error(s) in re-building vignettes:
--- re-building 'PrimarySchool.Rmd' using rmarkdown
Quitting from lines 21-33 (PrimarySchool.Rmd) 
Error: processing vignette 'PrimarySchool.Rmd' failed with diagnostics:
there is no package called 'igraph'
--- failed re-building 'PrimarySchool.Rmd'

--- re-building 'blogosphere.Rmd' using rmarkdown
Quitting from lines 22-32 (blogosphere.Rmd) 
Error: processing vignette 'blogosphere.Rmd' failed with diagnostics:
there is no package called 'igraph'
--- failed re-building 'blogosphere.Rmd'

--- re-building 'les_miserables.Rmd' using rmarkdown
Quitting from lines 18-22 (les_miserables.Rmd) 
Error: processing vignette 'les_miserables.Rmd' failed with diagnostics:
there is no package called 'igraph'
--- failed re-building 'les_miserables.Rmd'

SUMMARY: processing the following files failed:
  'PrimarySchool.Rmd' 'blogosphere.Rmd' 'les_miserables.Rmd'

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'devtools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gsDesign/gsDesign.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gsEasy/gsEasy.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'DiagrammeR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/GSE/GSE.Rcheck/00install.out' for details.
Package required but not available: 'Hmisc'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'imager'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gsignal/gsignal.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gsisdecoder/gsisdecoder.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gsl/gsl.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gsmoothr/gsmoothr.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'spelling', 'roxygen2'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gss/gss.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'dplyr'
  All declared Imports should be used.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'rgdal', 'sf', 'stars'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gstat/gstat.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gsw/gsw.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gsynth/gsynth.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gte/gte.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'units', 'sf', 'rgdal', 'lwgeom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking:
  'dodgr', 'leafem', 'lwgeom', 'mapview', 'sf'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gtfsrouter/gtfsrouter.Rcheck/00install.out' for details.
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.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'SGP', 'taxize'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gtools/gtools.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'rvest', 'xml2'
Note: found 116 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Note: found 269 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking:
  'flextable', 'Hmisc', 'huxtable', 'kableExtra', 'officer', 'spelling'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Note: found 40918 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking:
  'spdep', 'adegraphics', 'adespatial'
Error(s) in re-building vignettes:
--- re-building 'MultiSpat.Rmd' using rmarkdown
Quitting from lines 33-39 (MultiSpat.Rmd) 
Error: processing vignette 'MultiSpat.Rmd' failed with diagnostics:
there is no package called 'adegraphics'
--- failed re-building 'MultiSpat.Rmd'

--- re-building 'guerry-multivariate.Rmd' using rmarkdown
--- finished re-building 'guerry-multivariate.Rmd'

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

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
Running examples in 'GuessCompx-Ex.R' failed
The error most likely occurred in:

> ### Name: CompEst
> ### Title: Complexity Estimation and Prediction
> ### Aliases: CompEst
> 
> ### ** Examples
> 
> # Dummy function that mimics a constant time complexity and
> # N.log(N) memory complexity:
> f1 = function(df){
+   Sys.sleep(rnorm(1, 0.1, 0.02))
+   v = rnorm(n = nrow(df)*log(nrow(df))*(runif(1, 1e3, 1.1e3)))
+ }
> out = CompEst(d = mtcars, f = f1, replicates=2, start.size=2, max.time = 1)
Warning: 'memory.size()' is no longer supported
Warning: 'memory.size()' is no longer supported
Warning: 'memory.size()' is no longer supported
Warning: 'memory.size()' is no longer supported
Warning: 'memory.size()' is no longer supported
Warning: 'memory.size()' is no longer supported
Warning: 'memory.size()' is no longer supported
Warning: 'memory.size()' is no longer supported
Warning: 'memory.size()' is no longer supported
Warning: 'memory.size()' is no longer supported
Warning: 'memory.size()' is no longer supported
Warning: 'memory.size()' is no longer supported
Warning: 'memory.size()' is no longer supported
Warning: 'memory.size()' is no longer supported
Warning: 'memory.size()' is no longer supported
Warning: 'memory.size()' is no longer supported
Warning: 'memory.size()' is no longer supported
Warning: 'memory.size()' is no longer supported
Best model CONSTANT for time can be caused by not choosing a sufficiently high max.time value
warning: best TIME model not significantly different from a constant relationship. Increase max.time or replicates.
Warning in glm.fit(x = numeric(0), y = numeric(0), weights = NULL, start = NULL,  :
  no observations informative at iteration 1
Warning: glm.fit: algorithm did not converge
Error in glm.fit(x = numeric(0), y = numeric(0), weights = NULL, start = NULL,  : 
  object 'fit' not found
Calls: CompEst -> CompEstBenchmark -> glm -> eval -> eval -> glm.fit
Execution halted
Error(s) in re-building vignettes:
--- re-building 'GuessCompx.Rmd' using rmarkdown
Quitting from lines 60-62 (GuessCompx.Rmd) 
Error: processing vignette 'GuessCompx.Rmd' failed with diagnostics:
object 'fit' not found
--- failed re-building 'GuessCompx.Rmd'

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

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/GUILDS/GUILDS.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/GUniFrac/GUniFrac.Rcheck/00install.out' for details.
Package required but not available: 'units'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Note: found 13617 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/GUTS/GUTS.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'eda4treeR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/GWASExactHW/GWASExactHW.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
simCCCent : <anonymous>: no visible global function definition for
  'simulate.formula'
Undefined global functions or variables:
  simulate.formula
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
calculate.threshold: no visible global function definition for 'pchisq'
gwerAM: no visible global function definition for 'rnorm'
gwerAM: no visible binding for global variable 'quantile'
Undefined global functions or variables:
  pchisq quantile rnorm
Consider adding
  importFrom("stats", "pchisq", "quantile", "rnorm")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'spdep', 'GWmodel'

Package suggested but not available for checking: 'rgdal'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/GWEX/GWEX.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'rgdal'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/gwfa/gwfa.Rcheck/00install.out' for details.
normalweight: no visible binding for global variable 'NW_above'
normalweight: no visible binding for global variable 'NW_below'
obese: no visible global function definition for 'data'
obese: no visible binding for global variable 'OB_above'
obese: no visible binding for global variable 'OB_below'
overweight: no visible global function definition for 'data'
overweight: no visible binding for global variable 'OW_above'
overweight: no visible binding for global variable 'OW_below'
Undefined global functions or variables:
  NW_above NW_below OB_above OB_below OW_above OW_below data
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'RGtk2'

Package suggested but not available for checking: 'cairoDevice'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Namespaces in Imports field not imported from:
  'doParallel' 'foreach' 'spgwr'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'spatialreg', 'spdep'

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', 'sf', 'leaflet'

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: 'rlist', 'plotROC', 'kableExtra'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'library' or 'require' calls to packages already attached by Depends:
  'fields' 'lars'
  Please remove these calls from your code.
Package in Depends field not imported from: 'lars'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
gwl.beta: no visible global function definition for 'lars'
gwl.cv.err: no visible global function definition for 'lars'
gwl.est: no visible global function definition for 'lm'
gwr.bw.est: no visible global function definition for 'lm'
gwr.est: no visible global function definition for 'lm'
gwr.rsquare: no visible global function definition for 'cor'
gwrr.est: no visible global function definition for 'lm'
Undefined global functions or variables:
  cor lars lm
Consider adding
  importFrom("stats", "cor", "lm")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'officer', 'sf'

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.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/GxEScanR/GxEScanR.Rcheck/00install.out' for details.
GxMestimator: no visible global function definition for 'na.omit'
initialization_chol: no visible global function definition for 'cov'
initialization_corr: no visible global function definition for 'cov'
initialization_nlmain: no visible global function definition for
  'lm.fit'
print.summaryGxMclass: no visible global function definition for
  'pnorm'
print.summaryGxMclass: no visible global function definition for
  'printCoefmat'
Undefined global functions or variables:
  cov lm.fit na.omit pnorm printCoefmat
Consider adding
  importFrom("stats", "cov", "lm.fit", "na.omit", "pnorm",
             "printCoefmat")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'reticulate'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking: 'rgl', 'plot3Drgl'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Malformed Description field: should contain one or more complete sentences.
hf.bt: no visible global function definition for 'median'
Undefined global functions or variables:
  median
Consider adding
  importFrom("stats", "median")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'DiagrammeR'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'spelling'
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'pegas'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'spelling', 'vdiffr'
Namespaces in Imports field not imported from:
  'DT' 'gsubfn' 'stringr'
  All declared Imports should be used.
Running 'spelling.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(HaDeX)
  > 
  > test_check("HaDeX")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_comparison_plot.R:4:1): (code run outside of `test_that()`) ─────
  Error: there is no package called 'vdiffr'
  Backtrace:
      █
   1. └─base::library(vdiffr) test_comparison_plot.R:4:0
  ── Error (test_plot_coverage.R:3:1): (code run outside of `test_that()`) ───────
  Error: there is no package called 'vdiffr'
  Backtrace:
      █
   1. └─base::library(vdiffr) test_plot_coverage.R:3:0
  ── Error (test_plot_position_frequency.R:3:1): (code run outside of `test_that()`) ──
  Error: there is no package called 'vdiffr'
  Backtrace:
      █
   1. └─base::library(vdiffr) test_plot_position_frequency.R:3:0
  ── Error (test_woods_plot.R:4:1): (code run outside of `test_that()`) ──────────
  Error: there is no package called 'vdiffr'
  Backtrace:
      █
   1. └─base::library(vdiffr) test_woods_plot.R:4:0
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 33 ]
  Error: Test failures
  Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
hsTableReader: no visible global function definition for 'object.size'
hsWriteTable: no visible global function definition for 'write.table'
Undefined global functions or variables:
  object.size write.table
Consider adding
  importFrom("utils", "object.size", "write.table")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'tikzDevice', 'staplr'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/hadron/hadron.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'vdiffr'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/hal9001/hal9001.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages suggested but not available for checking: 'nbpMatching', 'Cairo'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'xml2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'devtools'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'igraph', 'png'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/hans/hans.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/hapassoc/hapassoc.Rcheck/00install.out' for details.
allele.marq: no visible global function definition for 'na.omit'
depart.LDL: no visible global function definition for 'aov'
freq.all: no visible global function definition for 'na.omit'
hapim.LD.add: no visible global function definition for 'optim'
hapim.LDL.add: no visible global function definition for 'optim'
obj.haplomax.HS.add: no visible global function definition for 'aov'
obj.haplomax.add: no visible global function definition for 'aov'
vrais.LD.add: no visible global function definition for 'dnorm'
vrais.LDL.add.pere: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  aov dnorm na.omit optim
Consider adding
  importFrom("stats", "aov", "dnorm", "na.omit", "optim")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/Haplin/Haplin.Rcheck/00install.out' for details.
Package required but not available: 'XML'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
AssignQTL : <anonymous>: no visible global function definition for
  'rgamma'
AssignSingleQTL: no visible global function definition for 'rgamma'
ListQTL : <anonymous>: no visible global function definition for
  'rgamma'
SampleBaseHaplotype: no visible global function definition for 'runif'
SampleHaplotype: no visible global function definition for 'rpois'
SampleHaplotype: no visible global function definition for 'runif'
SampleHaplotype: no visible global function definition for 'rbinom'
Undefined global functions or variables:
  rbinom rgamma rpois runif
Consider adding
  importFrom("stats", "rbinom", "rgamma", "rpois", "runif")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'rms'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'phangorn'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/hapsim/hapsim.Rcheck/00install.out' for details.
Packages suggested but not available for checking: 'devtools', 'roxygen2'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/HardyWeinberg/HardyWeinberg.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/HARModel/HARModel.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: 'Seurat'
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/harmony/harmony.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
File
  LICENSE
is not mentioned in the DESCRIPTION file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/hashr/hashr.Rcheck/00install.out' for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/haven/haven.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/hawkesbow/hawkesbow.Rcheck/00install.out' for details.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/hawkes/hawkes.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'jpeg'
'LazyData' is specified without a 'data' directory
Running examples in 'hazer-Ex.R' failed
The error most likely occurred in:

> ### Name: getBrightness
> ### Title: The brighness map of an image (0 to 1).
> ### Aliases: getBrightness
> 
> ### ** Examples
> 
> library(jpeg)
Error in library(jpeg) : there is no package called 'jpeg'
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(hazer)
  > 
  > test_check("hazer")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (testall.R:3:1): (code run outside of `test_that()`) ──────────────────
  Error: there is no package called 'jpeg'
  Backtrace:
      █
   1. └─base::library(jpeg) testall.R:3:0
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'detecting-hazy-images.Rmd' using rmarkdown
Quitting from lines 20-22 (detecting-hazy-images.Rmd) 
Error: processing vignette 'detecting-hazy-images.Rmd' failed with diagnostics:
there is no package called 'jpeg'
--- failed re-building 'detecting-hazy-images.Rmd'

SUMMARY: processing the following file failed:
  'detecting-hazy-images.Rmd'

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
extract_hazus_functions: no visible global function definition for
  'data'
Undefined global functions or variables:
  data
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'rstan', 'StanHeaders'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/hbmem/hbmem.Rcheck/00install.out' for details.
detect.movement: no visible global function definition for 't.test'
generate.random.conf: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  rnorm t.test
Consider adding
  importFrom("stats", "rnorm", "t.test")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: 'arm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Malformed Title field: should not end in a period.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/HBV.IANIGLA/HBV.IANIGLA.Rcheck/00install.out' for details.
Note: found 104392 marked UTF-8 strings
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
PoincarePlot: no visible global function definition for 'lines'
PoincarePlot: no visible global function definition for 'lowess'
hctest: no visible global function definition for 'cor.test'
rdplot: no visible global function definition for 'lines'
rdplot: no visible global function definition for 'lowess'
rdplot: no visible global function definition for 'rgb'
simer: no visible global function definition for 'runif'
simer: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  cor.test lines lowess rgb rnorm runif
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "lines")
  importFrom("stats", "cor.test", "lowess", "rnorm", "runif")
to your NAMESPACE file.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Installation failed.
See 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/hdbinseg/hdbinseg.Rcheck/00install.out' for details.