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Running ‘testthat.R’ [74s/137s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── Error ('test_exportOpenTiles.R:13:3'): exportDifferentials works on a 3 sample test dataset ──
  Error in `.stopOnAvailablePkg(genome)`: BSgenome.Hsapiens.UCSC.hg19 package is not currently installed.
    You first need to install it, which you can do with:
        library(BiocManager)
        install("BSgenome.Hsapiens.UCSC.hg19")
  Backtrace:
      ▆
   1. └─MOCHA::exportOpenTiles(...) at test_exportOpenTiles.R:13:3
   2.   └─BSgenome::getBSgenome(S4Vectors::metadata(SampleTileObject)$Genome)
   3.     └─BSgenome:::.getInstalledPkgnameFromGenome(genome, masked = masked)
   4.       └─BSgenome:::.stopOnAvailablePkg(genome)
  
  [ FAIL 2 | WARN 14 | SKIP 23 | PASS 21 ]
  Error: Test failures
  Execution halted
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--- re-building ‘NBLAST-Clustering.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
2023-07-10 21:31:32.757 R[43986:2287591920] XType: Using static font registry.

Quitting from lines 57-60 [unnamed-chunk-5] (NBLAST-Clustering.Rmd)
Error: processing vignette 'NBLAST-Clustering.Rmd' failed with diagnostics:
Saving a widget with selfcontained = TRUE requires pandoc. See here to learn more https://bookdown.org/yihui/rmarkdown-cookbook/install-pandoc.html
--- failed re-building ‘NBLAST-Clustering.Rmd’

SUMMARY: processing the following file failed:
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installed size is  6.1Mb
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Package suggested but not available for checking: ‘csampling’
checkRd: (-1) Dmean.Rd:62: Escaped LaTeX specials: \&
checkRd: (-1) Dvar.Rd:63: Escaped LaTeX specials: \&
Package unavailable to check Rd xrefs: ‘csampling’
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Running examples in ‘NMRphasing-Ex.R’ failed
The error most likely occurred in:

> ### Name: MPC_AAM
> ### Title: MPC_AAM
> ### Aliases: MPC_AAM
> 
> ### ** Examples
> 
> data("fdat")
> mpc_aam_phased1 <- MPC_AAM(fdat$frequency_domain)
Error in localMaximumSlidingWindow(x, winSize) : 
  DLL requires the use of native symbols
Calls: MPC_AAM ... getLocalMaximumCWT -> localMaximum -> localMaximumSlidingWindow
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘NMRphasing_vignette.rmd’ using rmarkdown

Quitting from lines 82-92 [unnamed-chunk-5] (NMRphasing_vignette.rmd)
Error: processing vignette 'NMRphasing_vignette.rmd' failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘NMRphasing_vignette.rmd’

SUMMARY: processing the following file failed:
  ‘NMRphasing_vignette.rmd’

Error: Vignette re-building failed.
Execution halted
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'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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Package suggested but not available for checking: ‘hurricaneexposuredata’
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checkRd: (-1) nppbib.Rd:28: Escaped LaTeX specials: \#
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installed size is 10.7Mb
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installed size is  6.3Mb
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GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is 21.0Mb
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installed size is  6.5Mb
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installed size is 10.1Mb
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installed size is  6.3Mb
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installed size is 12.9Mb
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installed size is  5.9Mb
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installed size is  6.5Mb
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installed size is 10.9Mb
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'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
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installed size is 92.1Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
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installed size is  5.3Mb
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'LazyData' is specified without a 'data' directory
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installed size is  6.8Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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installed size is  5.0Mb
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installed size is 47.2Mb
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GNU make is a SystemRequirements.
installed size is 39.6Mb
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GNU make is a SystemRequirements.
Package required but not available: ‘TCGAbiolinks’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'rhdf5', 'Rhdf5lib'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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installed size is  5.6Mb
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GNU make is a SystemRequirements.
installed size is  6.3Mb
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GNU make is a SystemRequirements.
installed size is 33.4Mb
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installed size is 10.7Mb
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installed size is  5.2Mb
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installed size is 204.5Mb
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GNU make is a SystemRequirements.
installed size is  7.2Mb
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Package suggested but not available for checking: ‘openNLPmodels.en’
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installed size is  6.6Mb
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installed size is 11.4Mb
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installed size is  6.9Mb
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installed size is 34.9Mb
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Package required but not available: ‘mixAK’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Problems with news in ‘NEWS.md’:
No news entries found.
Package suggested but not available for checking: ‘gurobi’
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installed size is  7.9Mb
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Malformed Title field: should not end in a period.
Package which this enhances but not available for checking: ‘gurobi’
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Package suggested but not available for checking: ‘gurobi’
Problems with news in ‘NEWS.md’:
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'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
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installed size is  5.8Mb
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installed size is  6.6Mb
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installed size is 10.0Mb
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installed size is 12.0Mb
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installed size is  5.2Mb
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Package suggested but not available for checking: ‘Rcplex’
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installed size is 10.2Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
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Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Changes
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checkRd: (-1) residuals_paco.Rd:10: Escaped LaTeX specials: \$
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Package which this enhances but not available for checking: ‘CorShrink’
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S3 methods shown with full name in documentation object 'pamr-internal':
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The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) btsdemo.Rd:22: Escaped LaTeX specials: \_
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Malformed Description field: should contain one or more complete sentences.
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installed size is  7.1Mb
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Error(s) in re-building vignettes:
--- re-building ‘partitionspaper.Rnw’ using Sweave
Loading required package: partitions
Error: processing vignette 'partitionspaper.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'partitionspaper.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘partitionspaper.Rnw’

--- re-building ‘scrabble.Rnw’ using Sweave
Error: processing vignette 'scrabble.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'scrabble.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘scrabble.Rnw’

--- re-building ‘setpartitions.Rnw’ using Sweave
Loading required package: partitions
Error: processing vignette 'setpartitions.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'setpartitions.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘setpartitions.Rnw’

SUMMARY: processing the following files failed:
  ‘partitionspaper.Rnw’ ‘scrabble.Rnw’ ‘setpartitions.Rnw’

Error: Vignette re-building failed.
Execution halted
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Package suggested but not available for checking: ‘anomalize’
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GNU make is a SystemRequirements.
installed size is 10.7Mb
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installed size is  6.8Mb
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installed size is  6.9Mb
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/pbdMPI.Rcheck/00install.out’ for details.
Package required but not available: ‘pbdMPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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'LazyData' is specified without a 'data' directory
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Malformed Description field: should contain one or more complete sentences.
installed size is  5.9Mb
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installed size is 140.0Mb
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GNU make is a SystemRequirements.
installed size is  5.0Mb
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Problems with news in ‘NEWS.md’:
No news entries found.
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'LazyData' is specified without a 'data' directory
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installed size is  7.3Mb
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checkRd: (-1) Peacock.test-package.Rd:28: Escaped LaTeX specials: \_
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installed size is 18.1Mb
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Packages suggested but not available for checking:
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Packages unavailable to check Rd xrefs: ‘fields’, ‘gstat’, ‘car’
installed size is 126.0Mb
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GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
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checkRd: (-1) breslow.Rd:27: Escaped LaTeX specials: \# \#
checkRd: (-1) my.bspline.Rd:38: Escaped LaTeX specials: \$ \$ \$
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installed size is  6.0Mb
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installed size is 10.2Mb
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    data   2.8Mb
    libs   7.0Mb
installed size is 51.2Mb
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checkRd: (-1) CAPM.RiskPremium.Rd:67: Escaped LaTeX specials: \&
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checkRd: (-1) managers.Rd:8: Escaped LaTeX specials: \&
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checkRd: (-1) jackal.Rd:32: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
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Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Fixed issues
'LazyData' is specified without a 'data' directory
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Package unavailable to check Rd xrefs: ‘lme4’
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checkRd: (-1) PatentsRD.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) PatentsRD.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) PatentsRDUS.Rd:4: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
installed size is 34.1Mb
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GNU make is a SystemRequirements.
Packages suggested but not available for checking: 'Biostrings', 'seqLogo'
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installed size is  7.7Mb
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Package unavailable to check Rd xrefs: ‘phase1RMD’
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Packages suggested but not available for checking:
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installed size is  5.4Mb
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Packages suggested but not available for checking: 'caret', 'xgboost'
installed size is  5.1Mb
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'library' or 'require' call to ‘RDCOMClient’ in package code.
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LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
installed size is  7.8Mb
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installed size is 22.1Mb
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'library' or 'require' calls in package code:
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  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.
Package suggested but not available for checking: ‘BRugs’
Package unavailable to check Rd xrefs: ‘BRugs’
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'batchelor', 'slingshot'
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'LazyData' is specified without a 'data' directory
installed size is 25.4Mb
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installed size is  5.7Mb
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Malformed Description field: should contain one or more complete sentences.
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'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
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'LazyData' is specified without a 'data' directory
installed size is 44.8Mb
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installed size is  5.8Mb
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installed size is 35.7Mb
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘quanteda.textmodels’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.5Mb
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Packages suggested but not available for checking: 'xcms', 'MSnbase'
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Spectra’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Problems with news in ‘NEWS.md’:
No news entries found.
Error(s) in re-building vignettes:
--- re-building ‘fullpres.Rnw’ using Sweave
Loading required package: rngWELL
This is randtoolbox. For an overview, type 'help("randtoolbox")'.
Warning in sobol(10^3, 2, scrambling = 1) :
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Warning in sobol(10^3, 2, scrambling = 2) :
  scrambling is currently disabled.
Warning in coll.test(runif, 2^7, 2^10, 1, echo = FALSE) :
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Warning in coll.test(congruRand, 2^8, 2^14, 1, echo = FALSE) :
  p-values will be approximated in the presence of low expected collision number.
Error: processing vignette 'fullpres.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'fullpres.tex' failed.
LaTeX errors:
! LaTeX Error: File `perpage.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.79 \MakePerPage
                 [1]{footnote}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘fullpres.Rnw’

--- re-building ‘shortintro.Rnw’ using Sweave
Loading required package: rngWELL
This is randtoolbox. For an overview, type 'help("randtoolbox")'.
Warning in RNGkind("default") :
  someone corrupted the random-number generator: re-initializing
Error: processing vignette 'shortintro.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'shortintro.tex' failed.
LaTeX errors:
! LaTeX Error: File `perpage.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.87 \MakePerPage
                 [1]{footnote}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘shortintro.Rnw’

SUMMARY: processing the following files failed:
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Error: Vignette re-building failed.
Execution halted
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'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building ‘RankAggreg.Rnw’ using Sweave
Loading required package: cluster
Package 'mclust' version 6.0.0
Type 'citation("mclust")' for citing this R package in publications.

Attaching package: ‘kohonen’

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

    map

Error: processing vignette 'RankAggreg.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'RankAggreg.tex' failed.
LaTeX errors:
! LaTeX Error: File `relsize.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.28 \usepackage
                [mathcal]{euscript}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘RankAggreg.Rnw’

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

Error: Vignette re-building failed.
Execution halted
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required and available but unsuitable versions:
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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installed size is  5.2Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.7Mb
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installed size is 68.5Mb
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GNU make is a SystemRequirements.
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'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'cairoDevice', 'RGtk2'
installed size is 10.6Mb
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checkRd: (-1) acquireAuditData.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) rattle.Rd:44: Escaped LaTeX specials: \_
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: ‘raybevel’
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installed size is  9.9Mb
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installed size is  5.4Mb
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GNU make is a SystemRequirements.
installed size is 58.4Mb
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GNU make is a SystemRequirements.
installed size is 60.1Mb
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GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rhdf5’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 12.2Mb
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installed size is 45.0Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 15.1Mb
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Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rrelaxiv’
'LazyData' is specified without a 'data' directory
installed size is 64.3Mb
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GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rrelaxiv’
'LazyData' is specified without a 'data' directory
installed size is 20.2Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 13.8Mb
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Package suggested but not available for checking: ‘rqubic’

Depends: includes the non-default packages:
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Adding so many packages to the search path is excessive and importing
selectively is preferable.
'LazyData' is specified without a 'data' directory
checkRd: (-1) RcmdrPlugin.MA-package.Rd:21: Escaped LaTeX specials: \&
checkRd: (-1) RcmdrPlugin.MA-package.Rd:23: Escaped LaTeX specials: \&
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Package suggested but not available for checking: ‘ROpenOffice’
Depends: includes the non-default packages:
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Adding so many packages to the search path is excessive and importing
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Packages suggested but not available for checking:
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/Rcplex.Rcheck/00install.out’ for details.
installed size is 21.0Mb
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installed size is  6.5Mb
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Specified C++11: please drop specification unless essential
installed size is  9.5Mb
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Problems with news in ‘NEWS.md’:
No news entries found.
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GNU make is a SystemRequirements.
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'LazyData' is specified without a 'data' directory
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Specified C++11: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/RcppMeCab.Rcheck/00install.out’ for details.
Specified C++11: please drop specification unless essential
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installed size is  6.4Mb
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GNU make is a SystemRequirements.
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installed size is 14.2Mb
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installed size is 18.7Mb
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installed size is  7.3Mb
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Specified C++11: please drop specification unless essential
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Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘evolMap’
Unavailable namespace imported from by a ':::' call: ‘evolMap’
  See the note in ?`:::` about the use of this operator.
Package required but not available: ‘rhdf5’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
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--- re-building ‘rDNAse.Rnw’ using Sweave
Loading required package: rDNAse
Error: processing vignette 'rDNAse.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'rDNAse.tex' failed.
LaTeX errors:
! LaTeX Error: File `tablefootnote.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.6 \usepackage
               [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘rDNAse.Rnw’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
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    data   1.5Mb
installed size is  9.9Mb
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Package suggested but not available for checking: ‘dataui’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
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'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 10.3Mb
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'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
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'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
installed size is  7.0Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
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Package suggested but not available for checking: ‘Rmpi’
installed size is 19.4Mb
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installed size is 12.5Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  7.3Mb
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installed size is 11.2Mb
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'LazyData' is specified without a 'data' directory
Package required but not available: ‘Rmpi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'cdparcoord', 'partools'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘Rcplex’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
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Package suggested but not available for checking: ‘ggpubr’
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installed size is  7.3Mb
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installed size is  9.5Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Problems with news in ‘NEWS.md’:
No news entries found.
Packages suggested but not available for checking: 'PADOG', 'GSVA'
Packages unavailable to check Rd xrefs: ‘GSVA’, ‘PADOG’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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checkRd: (-1) cast.Rd:46: Escaped LaTeX specials: \_
checkRd: (-1) as-data-frame-cast-df-v7.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) as-data-frame-cast-matrix-59.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) as-matrix-cast-df-bu.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) as-matrix-cast-matrix-2y.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) cast-9g.rd:19: Escaped LaTeX specials: \_ \_
checkRd: (-1) cast-9g.rd:41: Escaped LaTeX specials: \_
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checkRd: (-1) expand-kx.rd:15: Escaped LaTeX specials: \_
checkRd: (-1) reshape-4u.rd:17: Escaped LaTeX specials: \_ \_
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checkRd: (-1) rec.Rd:23: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Package required but not available: ‘BSgenome.Hsapiens.UCSC.hg38’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Unknown package ‘btergm’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 24.2Mb
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Problems with news in ‘NEWS.md’:
No news entries found.
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  sub-directories of 1Mb or more:
    data  14.1Mb
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
Running ‘testthat.R’ [64s/56s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
       ▆
    1. ├─testthat::expect_error(...) at test-forestry.R:48:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. └─Rforestry::forestry(x = iris[, -1], y = iris[, 1], seed = seed_i)
    7.   └─base::tryCatch(...)
    8.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    9.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   10.         └─value[[3L]](cond)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1422 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data      1.9Mb
    doc       1.2Mb
    extdata   1.9Mb
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 28.6Mb
  sub-directories of 1Mb or more:
    libs  27.4Mb
installed size is 32.6Mb
  sub-directories of 1Mb or more:
    doc     3.0Mb
    fonts   1.5Mb
    libs   24.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    doc          10.3Mb
    htmlwidgets   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'mimic.demo', 'eicu.demo'
Running examples in ‘ridge-Ex.R’ failed
The error most likely occurred in:

> ### Name: pvals
> ### Title: Compute p-values for ridgeLinear and ridgeLogistic models
> ### Aliases: pvals pvals.ridgeLinear pvals.ridgeLogistic
> ###   plot.pvalsRidgeLinear plot.pvalsRidgeLogistic print.pvalsRidgeLinear
> ###   print.pvalsRidgeLogistic
> 
> ### ** Examples
> 
> data(GenBin)
> mod <- logisticRidge(Phenotypes ~ ., data = as.data.frame(GenBin))

Execution halted
Specified C++11: please drop specification unless essential
installed size is 18.4Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs  16.0Mb
checkRd: (-1) acg.Rd:72: Escaped LaTeX specials: \&
checkRd: (-1) gorilla.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) grassmann.utest.Rd:63: Escaped LaTeX specials: \&
checkRd: (-1) macg.Rd:71: Escaped LaTeX specials: \&
checkRd: (-1) sphere.utest.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) stiefel.utest.Rd:64: Escaped LaTeX specials: \&
checkRd: (-1) wrap.landmark.Rd:41: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is 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 ‘RInside/libs/RInside.so’:
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘RInside.o’
File ‘RInside/libs/RInside.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CleanTempDir’,
    ‘R_DefParams’, ‘R_ReplDLLinit’, ‘R_RunExitFinalizers’,
    ‘R_SetParams’, ‘R_SignalHandlers’, ‘R_TempDir’, ‘Rf_endEmbeddedR’,
    ‘Rf_initEmbeddedR’, ‘run_Rmainloop’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data      3.2Mb
    extdata   1.3Mb
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  12.0Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘portfolioBacktest’
installed size is 21.8Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  20.3Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   8.7Mb
'LazyData' is specified without a 'data' directory
Found the following possibly unsafe calls:
File ‘rJava/R/import.R’:
  unlockBinding(IMPORTER, env = env)
  assignInNamespace(IMPORTER, importer, envir = env)
File ‘rJava/R/jinit.R’:
  unlockBinding(x, .env)
  unlockBinding(x, pe)
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  jri/src/Makefile.win
  jri/src/win32/Makefile
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
Note: information on .o files is not available
File ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/rJava.Rcheck/rJava/libs/rJava.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    java   4.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 56.0Mb
  sub-directories of 1Mb or more:
    include   3.4Mb
    libs     51.7Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.0Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.8Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    datasets  10.2Mb
installed size is 28.3Mb
  sub-directories of 1Mb or more:
    R     4.0Mb
    exe  23.8Mb
'LazyData' is specified without a 'data' directory
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    libs  18.6Mb
installed size is 24.7Mb
  sub-directories of 1Mb or more:
    extdata  24.0Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) Exponential.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) Gamma.Rd:80: Escaped LaTeX specials: \&
checkRd: (-1) college.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) college.Rd:15: Escaped LaTeX specials: \$
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    lemon   2.8Mb
    libs   17.0Mb
'LazyData' is specified without a 'data' directory
installed size is 106.7Mb
  sub-directories of 1Mb or more:
    libs  105.9Mb
GNU make is a SystemRequirements.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/rlibkriging.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'DoubletFinder', 'EnhancedVolcano', 'RcppPlanc', 'reactome.db'
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs  12.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
Specified C++11: please drop specification unless essential
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    rmd   6.0Mb
Found the following significant warnings:
  Warning: Software mark not found in path.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/RMark.Rcheck/00install.out’ for details.
Warning: Software mark not found in path.
         If you have mark executable, you will need to set MarkPath object to its location (e.g. MarkPath="C:/Users/Jeff Laake/Desktop"

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
installed size is 135.1Mb
  sub-directories of 1Mb or more:
    libs  134.7Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/RmecabKo.Rcheck/00install.out’ for details.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   6.0Mb
checkRd: (-1) cGARCHfilter-class.Rd:57: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHfit-class.Rd:59: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHsim-class.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHspec-class.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) cgarchsim-methods.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) goGARCHfilter-class.Rd:155: Escaped LaTeX specials: \&
checkRd: (-1) goGARCHfit-class.Rd:166: Escaped LaTeX specials: \&
checkRd: (-1) rmgarch-package.Rd:73: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R          1.0Mb
    libs       1.1Mb
    minizinc   3.3Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 39.4Mb
  sub-directories of 1Mb or more:
    libs  38.4Mb
installed size is 27.7Mb
  sub-directories of 1Mb or more:
    libs  27.6Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/Rmpi.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
installed size is 85.0Mb
  sub-directories of 1Mb or more:
    libs  84.4Mb
Package unavailable to check Rd xrefs: ‘cmdstanr’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
GNU make is a SystemRequirements.
installed size is 19.4Mb
  sub-directories of 1Mb or more:
    libs  18.2Mb
Package required but not available: ‘R4RNA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    libs  20.6Mb
Package suggested but not available for checking: ‘recount3’
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    doc    2.2Mb
Package suggested but not available for checking: ‘rnaturalearthhires’
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.1Mb
Malformed Title field: should not end in a period.
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    libs  18.8Mb
checkRd: (-1) NlistServersInCategory.Rd:11: Escaped LaTeX specials: \_
Packages which this enhances but not available for checking:
  'pbdMPI', 'Rmpi'
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
Packages unavailable to check Rd xrefs: ‘pbdMPI’, ‘Rmpi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 102.1Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs     99.9Mb
'LazyData' is specified without a 'data' directory
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    libs  12.7Mb
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    doc    1.7Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    R  11.2Mb
installed size is 18.4Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs  15.8Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
installed size is 19.9Mb
  sub-directories of 1Mb or more:
    libs  19.7Mb
Packages suggested but not available for checking:
  'affydata', 'hgu95av2cdf', 'beadarrayExampleData',
  'illuminaHumanv3.db'
Package suggested but not available for checking: ‘robustbase’
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building ‘RobPer_vignette.Rnw’ using Sweave
Loading required package: robustbase
Loading required package: quantreg
Loading required package: SparseM

Attaching package: 'SparseM'

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

    backsolve

Loading required package: splines
Loading required package: BB
Loading required package: rgenoud
##  rgenoud (Version 5.9-0.3, Build Date: 2022-04-19)
##  See http://sekhon.berkeley.edu/rgenoud for additional documentation.
##  Please cite software as:
##   Walter Mebane, Jr. and Jasjeet S. Sekhon. 2011.
##   ``Genetic Optimization Using Derivatives: The rgenoud package for R.''
##   Journal of Statistical Software, 42(11): 1-26. 
##

Error: processing vignette 'RobPer_vignette.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'RobPer_vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {thumbpdf,lmodern}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'RobPer_vignette.Rnw'

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

Error: Vignette re-building failed.
Execution halted
installed size is 97.2Mb
  sub-directories of 1Mb or more:
    libs  96.4Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘ivgets’
Package unavailable to check Rd xrefs: ‘ivgets’
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    libs  17.3Mb
Specified C++11: please drop specification unless essential
installed size is 27.1Mb
  sub-directories of 1Mb or more:
    libs  26.5Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   4.9Mb
'LazyData' is specified without a 'data' directory
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc               1.7Mb
    libs              5.1Mb
    simulationStudy   1.5Mb
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Packages suggested but not available for checking: 'car', 'HH'
Package unavailable to check Rd xrefs: ‘HH’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) performance.Rd:35: Escaped LaTeX specials: \#
checkRd: (-1) performance.Rd:36: Escaped LaTeX specials: \# \# \#
checkRd: (-1) performance.Rd:37: Escaped LaTeX specials: \# \#
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package required but not available: ‘Rcplex’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    doc  15.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
GNU make is a SystemRequirements.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R         3.7Mb
    extdata   2.7Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
sh: cmake: command not found
------------------ CMAKE NOT FOUND --------------------

CMake was not found on the PATH. Please install CMake:

 - installr::install.cmake()  (Windows; inside the R console)
 - yum install cmake          (Fedora/CentOS; inside a terminal)
 - apt install cmake          (Debian/Ubuntu; inside a terminal)
 - brew install cmake         (MacOS; inside a terminal with Homebrew)
 - port install cmake         (MacOS; inside a terminal with MacPorts)

Alternatively install CMake from: <https://cmake.org/>

-------------------------------------------------------


It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
sh: cmake: command not found
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
sh: cmake: command not found
sh: cmake: command not found
sh: cmake: command not found
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/ROracle.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘MBESS’
Specified C++11: please drop specification unless essential
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   2.7Mb
    libs   5.3Mb
'LazyData' is specified without a 'data' directory
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    R      5.1Mb
    libs   7.8Mb
Package suggested but not available for checking: ‘RandomFields’
installed size is 61.1Mb
  sub-directories of 1Mb or more:
    libs  59.9Mb
GNU make is a SystemRequirements.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    libs  20.2Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   5.9Mb
'LazyData' is specified without a 'data' directory
installed size is 52.1Mb
  sub-directories of 1Mb or more:
    libs  52.0Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   5.7Mb
'LazyData' is specified without a 'data' directory
installed size is 33.8Mb
  sub-directories of 1Mb or more:
    libs  32.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 89.4Mb
  sub-directories of 1Mb or more:
    libs  88.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   3.6Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'fields', 'qgraph'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs  13.0Mb
GNU make is a SystemRequirements.
Note: information on .o files is not available
File ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/Rserve.Rcheck/Rserve/libs/Rserve.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_exit’, possibly from ‘exit’ (C)
  Found ‘_rand’, possibly from ‘rand’ (C)
  Found ‘_random’, possibly from ‘random’ (C)
  Found ‘_sprintf’, possibly from ‘sprintf’ (C)
  Found ‘_srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API calls to R: ‘R_Consolefile’, ‘R_InputHandlers’,
    ‘R_Outputfile’, ‘R_TempDir’, ‘R_Visible’, ‘addInputHandler’,
    ‘ptr_R_Busy’, ‘ptr_R_ClearerrConsole’, ‘ptr_R_FlushConsole’,
    ‘ptr_R_ReadConsole’, ‘ptr_R_ResetConsole’, ‘ptr_R_ShowMessage’,
    ‘ptr_R_WriteConsole’, ‘ptr_R_WriteConsoleEx’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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'LazyData' is specified without a 'data' directory
installed size is 27.4Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
installed size is  7.3Mb
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Specified C++11: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
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installed size is 299.3Mb
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GNU make is a SystemRequirements.
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GNU make is a SystemRequirements.
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installed size is 37.8Mb
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installed size is 24.9Mb
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GNU make is a SystemRequirements.
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installed size is  5.9Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
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GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘Gviz’
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installed size is 100.2Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
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installed size is 28.6Mb
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GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘cmdstanr’
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GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
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'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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Non-standard license specification:
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Standardizable: FALSE
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘glmmADMB’
Package required but not available: ‘GSVAdata’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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matrixOps:
  function(e1, e2)
matrixOps.rvec:
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See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gpuR’
installed size is  5.2Mb
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installed size is 59.2Mb
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Problems with news in ‘NEWS.md’:
No news entries found.
S3 methods shown with full name in documentation object 'matmult':
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The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rWCVPdata’
installed size is  5.9Mb
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Package suggested but not available for checking: ‘partykit’
Package unavailable to check Rd xrefs: ‘partykit’
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'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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Packages suggested but not available for checking:
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Packages unavailable to check Rd xrefs: ‘BiocPkgTools’, ‘biocViews’
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installed size is  5.1Mb
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Malformed Title field: should not end in a period.
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'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 14.8Mb
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installed size is 12.3Mb
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Specified C++11: please drop specification unless essential
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checkRd: (-1) BootsChapt.Rd:38: Escaped LaTeX specials: \&
checkRd: (-1) SemiparChangePoint.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) schapt.Rd:44: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.8Mb
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Specified C++11: please drop specification unless essential
installed size is 15.0Mb
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘lme4’
Note: skipping ‘my-vignette.Rnw’ due to unavailable dependencies: 'lme4'
Specified C++11: please drop specification unless essential
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checkRd: (-1) SAM.Rd:67: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:59: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:84: Escaped LaTeX specials: \# \$
checkRd: (-1) samr.Rd:88: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:92: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:97: Escaped LaTeX specials: \#
checkRd: (-1) samr.assess.samplesize.plot.Rd:12: Escaped LaTeX specials: \#
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'LazyData' is specified without a 'data' directory
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Package required and available but unsuitable version: ‘pcaMethods’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
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GNU make is a SystemRequirements.
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
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'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Updated help pages with examples
    Updated conjugate model sampler
Specified C++11: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
Packages which this enhances but not available for checking:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) x.oreo.Rd:48: Escaped LaTeX specials: \_ \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
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Packages suggested but not available for checking:
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Packages unavailable to check Rd xrefs: ‘DropletUtils’, ‘Nebulosa’
Package required but not available: ‘glmGamPoi’

Package suggested but not available for checking: ‘Linnorm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
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Packages suggested but not available for checking:
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'LazyData' is specified without a 'data' directory
installed size is 18.0Mb
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Package required but not available: ‘LoomExperiment’

Packages suggested but not available for checking:
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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Package required and available but unsuitable version: ‘UCell’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘simplifyEnrichment’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘GSVA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
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Package unavailable to check Rd xrefs: ‘infercnv’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘oligoClasses’
checkRd: (-1) simulateSNPs.Rd:46: Escaped LaTeX specials: \& \& \&
checkRd: (-1) simulateSNPs.Rd:80: Escaped LaTeX specials: \& \& \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘glmGamPoi’
Error(s) in re-building vignettes:
--- re-building ‘intro.Rnw’ using Sweave
scuba 1.11-1 
Type ‘help(scuba)’ for an introduction 
Read the warnings in ‘help(scuba.disclaimer)’ 
For news about changes to the package, type ‘news(package='scuba')’
scuba 1.11-1 
Type ‘help(scuba)’ for an introduction 
Read the warnings in ‘help(scuba.disclaimer)’ 
For news about changes to the package, type ‘news(package='scuba')’

Attaching package: ‘scuba’

The following objects are masked _by_ ‘.GlobalEnv’:

    pedro902, pedro903, pedro904, pedro922, pedro943, pedro944,
    pedro945, pedro946, pedro948, pedro949, pedro950

Error: processing vignette 'intro.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'intro.tex' failed.
LaTeX errors:
! LaTeX Error: File `anysize.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.9 \marginsize
               {2cm}{2cm}{2cm}{2cm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘intro.Rnw’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
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Error(s) in re-building vignettes:
  ...
--- re-building ‘sdcSpatial.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
Quitting from lines 190-192 (sdcSpatial.Rmd) 
Error: processing vignette 'sdcSpatial.Rmd' failed with diagnostics:
different crs
--- failed re-building ‘sdcSpatial.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.9Mb
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Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 10.0Mb
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installed size is 89.4Mb
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Error(s) in re-building vignettes:
--- re-building ‘sdmvspecies.Rnw’ using Sweave
Loading required package: sp
[1] "/Volumes/Builds/packages/big-sur-x86_64/results/4.3/sdmvspecies.Rcheck/sdmvspecies/external/env/bio1.bil" 
[2] "/Volumes/Builds/packages/big-sur-x86_64/results/4.3/sdmvspecies.Rcheck/sdmvspecies/external/env/bio11.bil"
[3] "/Volumes/Builds/packages/big-sur-x86_64/results/4.3/sdmvspecies.Rcheck/sdmvspecies/external/env/bio12.bil"
[4] "/Volumes/Builds/packages/big-sur-x86_64/results/4.3/sdmvspecies.Rcheck/sdmvspecies/external/env/bio14.bil"
[5] "/Volumes/Builds/packages/big-sur-x86_64/results/4.3/sdmvspecies.Rcheck/sdmvspecies/external/env/bio16.bil"
[6] "/Volumes/Builds/packages/big-sur-x86_64/results/4.3/sdmvspecies.Rcheck/sdmvspecies/external/env/bio5.bil" 
[7] "/Volumes/Builds/packages/big-sur-x86_64/results/4.3/sdmvspecies.Rcheck/sdmvspecies/external/env/bio7.bil" 
Error: processing vignette 'sdmvspecies.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'sdmvspecies.tex' failed.
LaTeX errors:
! LaTeX Error: File `hanging.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.9 \usepackage
               [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘sdmvspecies.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building ‘sealasso.Rnw’ using Sweave
Loading required package: lars
Loaded lars 1.3

Error: processing vignette 'sealasso.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'sealasso.tex' failed.
LaTeX errors:
! LaTeX Error: File `anysize.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \marginsize
               {2.5cm}{2.5cm}{2.5cm}{2.5cm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘sealasso.Rnw’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  9.2Mb
  sub-directories of 1Mb or more:
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installed size is 19.2Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 18.1Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
installed size is  9.2Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.8Mb
  sub-directories of 1Mb or more:
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Packages required but not available: 'ggmsa', 'msa'

Package suggested but not available for checking: ‘org.Rn.eg.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rsbml’
Packages suggested but not available for checking:
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Package unavailable to check Rd xrefs: ‘ArrayExpress’
Packages suggested but not available for checking:
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Packages unavailable to check Rd xrefs: ‘flowClust’, ‘flowMerge’
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Rmpfr’
Package suggested but not available for checking: ‘Ecdat’
'LazyData' is specified without a 'data' directory
installed size is 34.5Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.0Mb
  sub-directories of 1Mb or more:
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Problems with news in ‘NEWS.md’:
No news entries found.
Package which this enhances but not available for checking: ‘semPlot’
Packages suggested but not available for checking: 'blavaan', 'emmeans'
Package unavailable to check Rd xrefs: ‘blavaan’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
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Specified C++11: please drop specification unless essential
installed size is 22.8Mb
  sub-directories of 1Mb or more:
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Specified C++11: please drop specification unless essential
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
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GNU make is a SystemRequirements.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   4.3Mb
Specified C++14: please drop specification unless essential
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘airway’
Packages suggested but not available for checking:
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installed size is 17.7Mb
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'LazyData' is specified without a 'data' directory
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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Package required but not available: ‘GSVA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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installed size is 14.5Mb
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    Version (Date)
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Packages required but not available: 'HTSSIP', 'phyloseq'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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Unavailable namespace imported from by a ':::' call: ‘kmndirs’
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Package unavailable to check Rd xrefs: ‘caret’
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GNU make is a SystemRequirements.
installed size is  5.3Mb
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Package required but not available: ‘GSVA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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There are ::: calls to the package's namespace in its code. A package
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Package required but not available: ‘GWASTools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/spaths.Rcheck/00install.out’ for details.
Package required but not available: ‘SpatialExperiment’

Packages suggested but not available for checking: 'rhdf5', 'HDF5Array'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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installed size is 51.9Mb
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GNU make is a SystemRequirements.
installed size is  6.1Mb
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Depends: includes the non-default packages:
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selectively is preferable.
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Adding so many packages to the search path is excessive and importing
selectively is preferable.
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Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
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  'spatstat.explore', 'nlme', 'rpart'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.geom', 'spatstat.random',
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Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is  5.5Mb
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Running examples in ‘speaq-Ex.R’ failed
The error most likely occurred in:

> ### Name: BWR
> ### Title: BW ratio calculation
> ### Aliases: BWR
> 
> ### ** Examples
> 
> res=makeSimulatedData();
> X=res$data;
> groupLabel=res$label;
> peakList <- detectSpecPeaks(X,
+                             nDivRange = c(128),
+                             scales = seq(1, 16, 2),
+                             baselineThresh = 50000,
+                             SNR.Th = -1,
+                             verbose=FALSE
+ );
> resFindRef<- findRef(peakList);
> refInd <- resFindRef$refInd;
> maxShift = 50;
> Y <- dohCluster(X,
+                 peakList = peakList,
+                 refInd = refInd,
+                 maxShift  = maxShift,
+                 acceptLostPeak = TRUE, verbose=FALSE);
Warning in min(peakList) :
  no non-missing arguments to min; returning Inf
Warning in max(peakList) :
  no non-missing arguments to max; returning -Inf
Error in startP:(minpeakList - 1) : result would be too long a vector
Calls: dohCluster -> .withMaxShift -> hClustAlign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘classic_speaq_vignette.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
2023-07-10 23:48:34.091 R[19637:2290508776] XType: Using static font registry.

Quitting from lines 111-120 [Spectral_alignment] (classic_speaq_vignette.Rmd)
Error: processing vignette 'classic_speaq_vignette.Rmd' failed with diagnostics:
result would be too long a vector
--- failed re-building ‘classic_speaq_vignette.Rmd’

--- re-building ‘speaq2_illustrations.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
2023-07-10 23:48:40.223 R[20964:2290511430] XType: Using static font registry.

Quitting from lines 71-83 [detect winepeaks] (speaq2_illustrations.Rmd)
Error: processing vignette 'speaq2_illustrations.Rmd' failed with diagnostics:
invalid 'times' argument
--- failed re-building ‘speaq2_illustrations.Rmd’

SUMMARY: processing the following files failed:
  ‘classic_speaq_vignette.Rmd’ ‘speaq2_illustrations.Rmd’

Error: Vignette re-building failed.
Execution halted
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Roadmap of specklestar package
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Undocumented S4 methods:
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  generic '[' and siglist 'SpectraInTime,missing,ANY,ANY'
  generic '[' and siglist 'SpectraInTime,missing,missing,ANY'
  generic '[' and siglist 'SpectraInTimeComp,ANY,ANY,ANY'
  generic '[' and siglist 'SpectraInTimeComp,ANY,missing,ANY'
  generic '[' and siglist 'SpectraInTimeComp,missing,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) image.plot.Rd:78: Escaped LaTeX specials: \$
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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.
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installed size is  7.1Mb
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installed size is  5.2Mb
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Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
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installed size is  5.4Mb
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Package suggested but not available for checking: ‘ggraph’
Problems with news in ‘NEWS.md’:
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'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Running examples in ‘spsurv-Ex.R’ failed
The error most likely occurred in:

> ### Name: bppo
> ### Title: Bernstein Polynomial Based Proportional Odds Model
> ### Aliases: bppo
> 
> ### ** Examples
> 
> 
> library("spsurv")
> data("veteran")
Warning in data("veteran") : data set ‘veteran’ not found
> 
> fit <- bppo(Surv(time, status) ~ karno + celltype,
+ data = veteran)
Error in optimHess(theta, fn, gr, control = list(fnscale = -1)) : 
  non-finite value supplied by optim
Calls: bppo ... spbp.mle -> <Anonymous> -> <Anonymous> -> .local -> optimHess
Execution halted
Running ‘testthat.R’ [17s/31s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── Error ('test.R:33:1'): (code run outside of `test_that()`) ──────────────────
  Error in `optimHess(theta, fn, gr, control = list(fnscale = -1))`: non-finite value supplied by optim
  Backtrace:
      ▆
   1. └─spsurv::bppo(Surv(time, status) ~ karno + factor(celltype), data = veteran) at test.R:33:0
   2.   └─spsurv:::spbp.default(...)
   3.     └─spsurv:::spbp.mle(standata = standata, ...)
   4.       ├─rstan::optimizing(...)
   5.       └─rstan::optimizing(...)
   6.         └─rstan (local) .local(object, ...)
   7.           └─stats::optimHess(theta, fn, gr, control = list(fnscale = -1))
  
  [ FAIL 1 | WARN 7 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
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GNU make is a SystemRequirements.
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installed size is  5.0Mb
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Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘SSsimple.Snw’ using Sweave
Loading required package: mvtnorm
Error: processing vignette 'SSsimple.Snw' failed with diagnostics:
Running 'texi2dvi' on 'SSsimple.tex' failed.
LaTeX errors:
! LaTeX Error: File `supertabular.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.8 \usepackage
               {wasysym}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘SSsimple.Snw’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
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installed size is 26.8Mb
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installed size is 17.4Mb
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GNU make is a SystemRequirements.
installed size is 92.5Mb
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GNU make is a SystemRequirements.
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Package which this enhances but not available for checking: ‘CVXR’
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installed size is  6.4Mb
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checkRd: (-1) multiCUMSUM.Rd:33: Escaped LaTeX specials: \&
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installed size is  6.9Mb
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Specified C++11: please drop specification unless essential
installed size is  9.8Mb
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Package suggested but not available for checking: ‘asreml’
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installed size is  5.0Mb
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installed size is  7.3Mb
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installed size is  7.5Mb
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Package unavailable to check Rd xrefs: ‘tweedie’
Found the following possibly unsafe calls:
File ‘statnet.common/R/control.utilities.R’:
  unlockBinding("snctrl", environment(snctrl))
  unlockBinding("snctrl", environment(update_my_snctrl))
Package suggested but not available for checking: ‘networksis’
unable to reach CRAN

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
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checkRd: (-1) stdGlm.Rd:93: Escaped LaTeX specials: \&
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No news entries found.
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installed size is  5.9Mb
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Error(s) in re-building vignettes:
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--- re-building ‘StMoMoVignette.Rnw’ using Sweave
Loading required package: gnm
Loading required package: forecast
Error: processing vignette 'StMoMoVignette.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'StMoMoVignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `ctable.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.7 \usepackage
               [caption = false]{subfig}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'StMoMoVignette.Rnw'

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

Error: Vignette re-building failed.
Execution halted
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GNU make is a SystemRequirements.
installed size is  6.2Mb
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installed size is  7.8Mb
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installed size is  9.2Mb
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installed size is 26.8Mb
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Malformed Title field: should not end in a period.
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installed size is  9.3Mb
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installed size is 10.5Mb
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installed size is 10.3Mb
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Package unavailable to check Rd xrefs: ‘HDoutliers’
installed size is 13.0Mb
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Malformed Title field: should not end in a period.
Specified C++11: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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installed size is 34.6Mb
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Package suggested but not available for checking: ‘STRaitRazoR’
efpFunctional: multiple local function definitions for ‘plotProcess’
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mefp.efp: multiple local function definitions for ‘computeEmpProc’ with
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Package required but not available: ‘GSVA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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installed size is  8.0Mb
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installed size is 52.3Mb
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GNU make is a SystemRequirements.
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Package suggested but not available for checking: ‘INLA’
installed size is  5.9Mb
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installed size is 10.1Mb
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Packages suggested but not available for checking:
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installed size is 14.9Mb
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installed size is 65.0Mb
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GNU make is a SystemRequirements.
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Problems with news in ‘NEWS.md’:
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    Amendments to functions
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Problems with news in ‘NEWS.md’:
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    pre-release switchboard (2020 - 2021)
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GNU make is a SystemRequirements.
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'LazyData' is specified without a 'data' directory
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installed size is 10.3Mb
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Problems with news in ‘NEWS.md’:
No news entries found.
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LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Packages required but not available: 'microbiome', 'phyloseq'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
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Package unavailable to check Rd xrefs: ‘dearseq’
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Malformed Description field: should contain one or more complete sentences.
installed size is  7.4Mb
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installed size is 35.0Mb
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GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  6.7Mb
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Package which this enhances but not available for checking: ‘R2wd’
Unknown package ‘teal’ in Rd xrefs
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
installed size is 27.9Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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checkRd: (-1) CPdimensionalityplot.Rd:18: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: ‘ggplot2’
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Package suggested but not available for checking: ‘lme4’
Problems with news in ‘NEWS.md’:
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installed size is  6.9Mb
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checkRd: (-1) compare.Rd:46: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
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Packages suggested but not available for checking:
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'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
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GNU make is a SystemRequirements.
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GNU make is a SystemRequirements.
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Packages suggested but not available for checking:
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'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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Package required but not available: ‘EnhancedVolcano’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
--- re-building ‘ToolsForCoDa.Rnw’ using Sweave
Loading required package: mice

Attaching package: 'mice'

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

    filter

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

    cbind, rbind

Loading required package: Rsolnp
Loading required package: nnet
Loading required package: MASS
Loading required package: calibrate
Error: processing vignette 'ToolsForCoDa.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'ToolsForCoDa.tex' failed.
LaTeX errors:
! LaTeX Error: File `wasysym.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.10 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'ToolsForCoDa.Rnw'

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘stm’
Package unavailable to check Rd xrefs: ‘stm’
Packages suggested but not available for checking:
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Package suggested but not available for checking: ‘gurobi’
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘toscaData’
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Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: ‘competitiontoolbox’
Package unavailable to check Rd xrefs: ‘competitiontoolbox’
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Note: skipping ‘tramvs.Rnw’ due to unavailable dependencies: 'tramnet'
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Specified C++11: please drop specification unless essential
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Package which this enhances but not available for checking: ‘fwelnet’
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'LazyData' is specified without a 'data' directory
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checkRd: (-1) dcc.Rd:227: Escaped LaTeX specials: \&
checkRd: (-1) seascorr.Rd:128: Escaped LaTeX specials: \&
Package required but not available: ‘phyloseq’

Package suggested but not available for checking: ‘adaptiveGPCA’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘TreeDistData’
installed size is  7.8Mb
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Package suggested but not available for checking: ‘Seurat’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
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installed size is  5.2Mb
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Package suggested but not available for checking: ‘brms’
Package unavailable to check Rd xrefs: ‘brms’
installed size is 18.7Mb
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Problems with news in ‘NEWS.md’:
No news entries found.
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GNU make is a SystemRequirements.
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Specified C++11: please drop specification unless essential
installed size is 39.5Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'rrelaxiv', 'gurobi'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/triptych.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
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GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  8.3Mb
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There are ::: calls to the package's namespace in its code. A package
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Package unavailable to check Rd xrefs: ‘fpc’
Error(s) in re-building vignettes:
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--- re-building ‘tsglm.Rnw’ using Sweave
Error: processing vignette 'tsglm.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'tsglm.tex' failed.
LaTeX errors:
! LaTeX Error: File `mathabx.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.13 \usepackage
                {microtype}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'tsglm.Rnw'

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  9.8Mb
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checkRd: (-1) TempDisaggDGP.Rd:79: Escaped LaTeX specials: \&
checkRd: (-1) disaggregate.Rd:56: Escaped LaTeX specials: \&
installed size is 44.1Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  8.5Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 96.9Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  5.7Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package unavailable to check Rd xrefs: ‘twang’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘sl3’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is  7.2Mb
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installed size is 110.0Mb
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GNU make is a SystemRequirements.
installed size is 19.8Mb
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installed size is  8.2Mb
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Specified C++11: please drop specification unless essential
installed size is 27.2Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
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Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    uktrans_get is fixed when start_date is used (#2)
    Extra layer of of NULL returns to fail gracefully with an informative message.
    Removed travis & appveyor and using gh_actions instead.
    Using gh-pages to create the pkgdown website.
    Create an app as vignette page to search with the help of uklr.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
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'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 14.0Mb
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2023-11-27 06:51:56.302 R[14525:2096614800] XType: Using static font registry.

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
2023-11-27 06:51:58.157 R[15369:2096616534] XType: Using static font registry.
2023-11-27 06:52:00.054 R[16081:2096617951] XType: Using static font registry.
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
2023-11-27 06:52:02.337 R[16881:2096619572] XType: Using static font registry.
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
2023-11-27 06:52:04.198 R[17365:2096620546] XType: Using static font registry.
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
2023-11-27 06:52:07.135 R[18482:2096622832] XType: Using static font registry.
2023-11-27 06:52:13.295 R[20905:2096627616] XType: Using static font registry.
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
2023-11-27 06:52:15.181 R[21482:2096628821] XType: Using static font registry.
2023-11-27 06:52:16.786 R[22130:2096630090] XType: Using static font registry.
2023-11-27 06:52:18.255 R[22695:2096631227] XType: Using static font registry.
2023-11-27 06:52:20.449 R[23405:2096632632] XType: Using static font registry.
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++14: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 52.0Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  8.1Mb
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘adespatial’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘USA.state.boundaries.data’
installed size is  7.2Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
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checkRd: (-1) aosat.Rd:20: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) aosat.Rd:21: Escaped LaTeX specials: \_
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installed size is  7.3Mb
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Malformed Title field: should not end in a period.
Specified C++11: please drop specification unless essential
installed size is 14.2Mb
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installed size is 39.1Mb
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Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'vaers', 'vaersND'
Packages suggested but not available for checking: 'vaers', 'vaersND'
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installed size is 24.7Mb
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installed size is  9.4Mb
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Problems with news in ‘NEWS.md’:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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checkRd: (-1) randomVarImpsRFplot.Rd:97: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
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installed size is  7.9Mb
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'LazyData' is specified without a 'data' directory
installed size is 10.3Mb
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GNU make is a SystemRequirements.
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Package suggested but not available for checking: ‘ggtern’
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checkRd: (-1) value.Rd:32: Escaped LaTeX specials: \$ \$
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Missing link or links in documentation object 'bigamma.mckay.Rd':
  ‘[VGAM]{gammaff.mm}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
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GNU make is a SystemRequirements.
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Package unavailable to check Rd xrefs: ‘INLA’
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GNU make is a SystemRequirements.
installed size is 57.0Mb
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GNU make is a SystemRequirements.
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S3 methods shown with full name in documentation object 'QIC.gee':
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The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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    Major changes
    Minor changes
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Warning in initDict() :
  cannot find WordNet 'dict' directory: please set the environment variable WNHOME to its parent

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
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GNU make is a SystemRequirements.
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GNU make is a SystemRequirements.
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Running examples in 'ACEP-Ex.R' failed
The error most likely occurred in:

> ### Name: acep_clean
> ### Title: Limpieza de texto.
> ### Aliases: acep_clean
> ### Keywords: normalizacion
> 
> ### ** Examples
> 
> acep_clean("El SUTEBA fue al paro. Reclaman mejoras salariales.", rm_cesp = FALSE)
Warning in readRDS(url("https://observatoriodeconflictividad.org/basesdatos/tildes.rds")) :
  URL 'https://observatoriodeconflictividad.org/basesdatos/tildes.rds': Timeout of 60 seconds was reached
Error in readRDS(url("https://observatoriodeconflictividad.org/basesdatos/tildes.rds")) : 
  cannot open the connection to 'https://observatoriodeconflictividad.org/basesdatos/tildes.rds'
Calls: acep_clean -> tryCatch -> tryCatchList -> readRDS
Execution halted
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Malformed Description field: should contain one or more complete sentences.
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checkRd: (-1) UN1.Rd:16: Escaped LaTeX specials: \$
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Running 'spelling.R' [0s]
  Running 'testthat.R' [11s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(applicable)
  Loading required package: ggplot2
  > 
  > test_check("applicable")
  Loading required package: dplyr
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  
  Attaching package: 'recipes'
  
  The following object is masked from 'package:stats':
  
      step
  
  
  Attaching package: 'proxyC'
  
  The following object is masked from 'package:stats':
  
      dist
  
  [ FAIL 1 | WARN 0 | SKIP 22 | PASS 92 ]
  
  ══ Skipped tests (22) ══════════════════════════════════════════════════════════
  • On CRAN (22): 'test-hat_values-fit.R:15:3', 'test-hat_values-fit.R:21:3',
    'test-hat_values-fit.R:111:3', 'test-hat_values-fit.R:123:3',
    'test-hat_values-score.R:2:3', 'test-hat_values-score.R:9:3',
    'test-hat_values-score.R:17:3', 'test-isolation-fit.R:38:3',
    'test-misc.R:3:3', 'test-pca-fit.R:21:3', 'test-pca-fit.R:27:3',
    'test-pca-score.R:2:3', 'test-pca-score.R:9:3', 'test-pca-score.R:17:3',
    'test-print.R:4:3', 'test-print.R:36:3', 'test-similarity.R:117:3',
    'test-similarity.R:128:3', 'test-similarity.R:147:3',
    'test-similarity.R:171:3', 'test-similarity.R:186:3',
    'test-similarity.R:202:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-isolation-fit.R:29:3'): model fitting for isolation forests ──
  res_rec$model$params$ndim (`actual`) not equal to 2 (`expected`).
  
    `actual`: 1
  `expected`: 2
  
  [ FAIL 1 | WARN 0 | SKIP 22 | PASS 92 ]
  Error: Test failures
  Execution halted
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checkRd: (-1) breast_cancer_clean_features.Rd:45: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
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checkRd: (-1) ec2_create_security_group.Rd:66: Escaped LaTeX specials: \#
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checkRd: (-1) ec2_create_security_group.Rd:79: Escaped LaTeX specials: \$
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installed size is  5.5Mb
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'LazyData' is specified without a 'data' directory
checkRd: (-1) barcode.Rd:52: Escaped LaTeX specials: \&
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Problems with news in 'NEWS.md':
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checkRd: (-1) personality.Rd:17: Escaped LaTeX specials: \$
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GNU make is a SystemRequirements.
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GNU make is a SystemRequirements.
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GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
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GNU make is a SystemRequirements.
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GNU make is a SystemRequirements.
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S3 methods shown with full name in documentation object 'export.bce':
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The \usage entries for S3 methods should use the \method markup and not
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See chapter 'Writing R documentation files' in the 'Writing R
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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checkRd: (-1) bgmm-package.Rd:23: Escaped LaTeX specials: \&
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Package suggested but not available for checking: 'INLA'
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GNU make is a SystemRequirements.
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Specified C++11: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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GNU make is a SystemRequirements.
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S3 methods shown with full name in documentation object 'select.cfs':
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See chapter 'Writing R documentation files' in the 'Writing R
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Depends: includes the non-default packages:
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checkRd: (-1) FighterAircraft.Rd:32: Escaped LaTeX specials: \&
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GNU make is a SystemRequirements.
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'LazyData' is specified without a 'data' directory
install_blat: no visible global function definition for 'download.file'
install_blat: no visible global function definition for 'unzip'
Undefined global functions or variables:
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Consider adding
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Package suggested but not available for checking: 'cmdstanr'
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GNU make is a SystemRequirements.
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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GNU make is a SystemRequirements.
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GNU make is a SystemRequirements.
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'LazyData' is specified without a 'data' directory
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Problems with news in 'NEWS.md':
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'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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See 'd:/Rcompile/CRANpkg/local/4.3/BRugs.Rcheck/00install.out' for details.
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checkRd: (-1) kink_estimator.Rd:60: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
checkRd: (-1) deleteZeroComponents.Rd:70: Escaped LaTeX specials: \& \&
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'LazyData' is specified without a 'data' directory
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Problems with news in 'NEWS.md':
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'LazyData' is specified without a 'data' directory
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checkRd: (-1) States.Rd:48: Escaped LaTeX specials: \$
Problems with news in 'NEWS.md':
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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checkRd: (-1) tpcExample.Rd:30: Escaped LaTeX specials: \&
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GNU make is a SystemRequirements.
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Problems with news in 'NEWS.md':
No news entries found.
Specified C++11: please drop specification unless essential
Packages which this enhances but not available for checking:
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'LazyData' is specified without a 'data' directory
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Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
Problems with news in 'NEWS.md':
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: 'countreg'
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Package suggested but not available for checking: 'cmdstanr'
Package unavailable to check Rd xrefs: 'cmdstanr'
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'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    clhs_0.7-2
    clhs_0.7-0
    clhs_0.6-0
    clhs_0.5-7
    clhs_0.5-6
    clhs_0.5-3
    clhs_0.5-2
    clhs_0.5-1
    clhs_0.5-0
    clhs_0.4-3
    clhs_0.4-2
    clhs_0.4-1
    clhs_0.4-0
    clhs_0.3-2
    clhs_0.3-1
    clhs_0.3-0
    clhs_0.2-1
    clhs_0.2-0
    clhs_0.1-0
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    doc    1.9Mb
installed size is 48.6Mb
  sub-directories of 1Mb or more:
    extdata  48.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
checkRd: (-1) clme.Rd:84: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) dtmvnom.Rd:30: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.predict.crrQR.Rd:18: Escaped LaTeX specials: \#
checkRd: (-1) plot.predict.crrQR.Rd:22: Escaped LaTeX specials: \#
checkRd: (-1) plot.predict.crr.Rd:18: Escaped LaTeX specials: \#
checkRd: (-1) plot.predict.crr.Rd:22: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'tobit1'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       3.2Mb
    extdata   1.7Mb
Package suggested but not available for checking: 'PopGenome'
Package suggested but not available for checking: 'disttree'
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'rkward'
Package which this enhances but not available for checking: 'rkward'
Package suggested but not available for checking: 'userfriendlyscience'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   2.5Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc       2.4Mb
    extdata   2.0Mb
Unexported object imported by a ':::' call: 'crayon:::mypaste'
  See the note in ?`:::` about the use of this operator.
Problems with news in 'NEWS.md':
No news entries found.
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    java   6.7Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'CAM'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) babies.Rd:35: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
run_pipeline_gbq: no visible global function definition for
  'query_exec'
Undefined global functions or variables:
  query_exec
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'conosPanel', 'p2data'
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc             2.2Mb
    vignette_data   2.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'cec2005benchmark', 'cec2013'
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   3.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 18.0Mb
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    extdata  17.7Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc   6.7Mb
checkRd: (-1) cosmoFns-package.Rd:34: Escaped LaTeX specials: \&
installed size is  5.1Mb
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    data   3.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    extdata   2.6Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    2.9Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'BSgenome.Scerevisiae.UCSC.sacCer3'
installed size is  6.5Mb
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    doc   6.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
Package suggested but not available for checking: 'INLA'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    doc    1.5Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   7.9Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   1.7Mb
    libs   7.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   5.8Mb
File 'curl/libs/x64/curl.dll':
  Found non-API call to R: 'R_new_custom_connection'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Running 'engine.R' [0s]
  Comparing 'engine.Rout' to 'engine.Rout.save' ...4d3
< Using libcurl 8.3.0 with Schannel
  Running 'spelling.R' [0s]
  Running 'testthat.R' [55s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(curl)
  Using libcurl 8.3.0 with Schannel
  > 
  > # Comply with CRAN policy: skip tests if no internet
  > if(curl::has_internet()){
  +   test_check("curl")
  + }
  This is libcurl version 8.3.0 with (OpenSSL/3.1.2) Schannel 
  Using test server: https://hb.r-universe.dev 
  [ FAIL 1 | WARN 0 | SKIP 4 | PASS 219 ]
  
  ══ Skipped tests (4) ═══════════════════════════════════════════════════════════
  • On CRAN (4): 'test-idn.R:6:3', 'test-multi-download.R:4:3',
    'test-seek.R:4:3', 'test-winssl.R:4:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-handle.R:137:3'): Custom URL parser ──────────────────────────
  `curl_fetch_memory("https://httpbin.org/delay/10", handle = h)` did not throw an error.
  
  [ FAIL 1 | WARN 0 | SKIP 4 | PASS 219 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Misc
checkRd: (-1) abs_d_ppv_npv.Rd:27: Escaped LaTeX specials: \_ \_ \_
Package which this enhances but not available for checking: 'RGtk2'
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages which this enhances but not available for checking:
  'Rcplex', 'gurobi', 'rcbc'
installed size is  6.4Mb
  sub-directories of 1Mb or more:
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    doc    1.2Mb
    libs   1.2Mb
Problems with news in 'NEWS.md':
No news entries found.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata       1.3Mb
    htmlwidgets   1.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'doMC'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    java   7.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'SASxport'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Package suggested but not available for checking: 'BRugs'
Package suggested but not available for checking: 'INLA'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Changes from previous package DecompHoriuchi
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.1Mb
    help   1.3Mb
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checkRd: (-1) scramb.Rd:44: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
checkRd: (-1) DendSer.Rd:50: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc       4.8Mb
    extdata   2.1Mb
Package suggested but not available for checking: 'Rdonlp2'
checkRd: (-1) discrimination.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) fitdmm.Rd:59: Escaped LaTeX specials: \$
Package suggested but not available for checking: 'Rdonlp2'
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checkRd: (-1) barriers.Rd:127: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.N' '.Nmiss' '.Q1' '.Q3' '.factorN' '.factorNmiss' '.factorQ1'
  '.factorQ3' '.factormax' '.factormean' '.factormedian' '.factormin'
  '.factorsd' '.max' '.mean' '.median' '.min' '.sd'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'RDCOMClient'
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    1.8Mb
    help   1.6Mb
    libs   1.2Mb
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data          1.8Mb
    htmlwidgets   3.6Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'signatureSearchData'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    doc  10.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'rrelaxiv'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) TempDisaggDGP.Rd:79: Escaped LaTeX specials: \&
checkRd: (-1) disaggregate.Rd:56: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'INLA'
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) dataCensoring.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) dataLong.Rd:170: Escaped LaTeX specials: \&
checkRd: (-1) dataLongCompRisksTimeDep.Rd:130: Escaped LaTeX specials: \&
checkRd: (-1) dataLongMultiSpell.Rd:123: Escaped LaTeX specials: \&
checkRd: (-1) dataLongTimeDep.Rd:96: Escaped LaTeX specials: \&
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   4.2Mb
Package which this enhances but not available for checking: 'INLA'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) booter.Rd:68: Escaped LaTeX specials: \&
checkRd: (-1) ci.booted.Rd:53: Escaped LaTeX specials: \&
checkRd: (-1) pbooter.Rd:57: Escaped LaTeX specials: \&
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'BOLTSSIRR'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    include  15.8Mb
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    libs  13.7Mb
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Changes to previous versions
    Minor changes
    Fixes
    Previous Versions
checkRd: (-1) dlsem.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) unirootTest.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) unirootTest.Rd:20: Escaped LaTeX specials: \&
checkRd: (-1) unirootTest.Rd:26: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) dnr.Rd:12: Escaped LaTeX specials: \#
S3 methods shown with full name in documentation object 'add.joint.mean.many':
  'all.cond.mean.PO' 'all.cond.mean2.PO'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Specified C++11: please drop specification unless essential
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc    6.5Mb
    libs   1.7Mb
GNU make is a SystemRequirements.
Package which this enhances but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R         2.1Mb
    data      2.0Mb
    extdata   2.3Mb
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    New features
Specified C++11: please drop specification unless essential
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S3 methods shown with full name in documentation object 'summary.error_interval':
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.run: no visible binding for global variable 'init'
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GNU make is a SystemRequirements.
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Installation failed.
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GNU make is a SystemRequirements.
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'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
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Malformed Description field: should contain one or more complete sentences.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    fonts   6.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Previous versions (not tagged nor released)
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'RandomFields'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) MultiAsset.Rd:26: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R   5.6Mb
Packages suggested but not available for checking: 'dggrids', 'INLA'
installed size is 20.8Mb
  sub-directories of 1Mb or more:
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    doc    1.8Mb
    libs  13.0Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'extraTrees', 'foba', 'nodeHarvest', 'obliqueRF', 'relaxo', 'rrlda'
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Spec_compare_localize_freq.Rd:49: Escaped LaTeX specials: \&
checkRd: (-1) Spec_compare_localize_freq.Rd:52: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    help   4.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
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installed size is 33.6Mb
  sub-directories of 1Mb or more:
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    libs   1.2Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      2.9Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) fitgbd.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) fitgld.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) gb.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) gbd.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) gld.Rd:36: Escaped LaTeX specials: \&
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.
checkRd: (-1) estprops.Rd:40: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'paleofire'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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installed size is 106.0Mb
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installed size is 103.1Mb
  sub-directories of 1Mb or more:
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    proj   8.4Mb
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
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    extdata   3.0Mb
Package suggested but not available for checking: 'gdxrrw'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'genderdata'
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is 13.6Mb
  sub-directories of 1Mb or more:
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Error(s) in re-building vignettes:
--- re-building 'geoAr_geofacet.Rmd' using rmarkdown
File figure/tucmap-1.png not found in resource path
Error: processing vignette 'geoAr_geofacet.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'geoAr_geofacet.Rmd'

--- re-building 'geoAr_leaflet.Rmd' using rmarkdown
File figure/map-1.png not found in resource path
Error: processing vignette 'geoAr_leaflet.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'geoAr_leaflet.Rmd'

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

SUMMARY: processing the following files failed:
  'geoAr_geofacet.Rmd' 'geoAr_leaflet.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
    libs      1.4Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc       2.1Mb
    extdata   3.5Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'geomarocdata'
'LazyData' is specified without a 'data' directory
installed size is 14.6Mb
  sub-directories of 1Mb or more:
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    extdata   2.5Mb
    help      2.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'RandomFields'

Package which this enhances but not available for checking: 'INLA'
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'RGtk2'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc       3.0Mb
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    libs      1.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    doc   7.0Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) boot_eip.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) constrained.Rd:93: Escaped LaTeX specials: \&
checkRd: (-1) constrained.Rd:37: Escaped LaTeX specials: \&
':::' call which should be '::': 'scales:::censor'
  See the note in ?`:::` about the use of this operator.
Unexported object imported by a ':::' call: 'productplots:::bound'
  See the note in ?`:::` about the use of this operator.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    2.3Mb
    help   1.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'lixoftConnectors'
installed size is  8.8Mb
  sub-directories of 1Mb or more:
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    help       2.4Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   3.9Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
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Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    * Changes all data options to .data to decrease possibility of column naming overlap
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Win CRAN check results - R Windows
installed size is 11.0Mb
  sub-directories of 1Mb or more:
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    help   1.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 18.0Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
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    help   2.5Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.UCSC.hg18.masked',
  'BSgenome.Hsapiens.UCSC.hg19.masked'
Specified C++11: please drop specification unless essential
checkRd: (-1) randPIT.Rd:52: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'doMC'
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installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   4.2Mb
checkRd: (-1) glmc.Rd:232: Escaped LaTeX specials: \&
checkRd: (-1) glmc.Rd:241: Escaped LaTeX specials: \&
checkRd: (-1) glmc.control.Rd:29: Escaped LaTeX specials: \$
checkRd: (-1) glmc.control.Rd:31: Escaped LaTeX specials: \$
checkRd: (-1) glmc.summaries.Rd:79: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    doc             1.3Mb
    libs            4.4Mb
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    vignette_data   1.1Mb
checkRd: (-1) coef.glmulti.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:27: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:51: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:60: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:61: Escaped LaTeX specials: \&
checkRd: (-1) consensus.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) getfit.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) glmulti-class.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) glmulti.Rd:99: Escaped LaTeX specials: \&
checkRd: (-1) summary.glmulti.Rd:72: Escaped LaTeX specials: \&
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'doMC'
'LazyData' is specified without a 'data' directory
checkRd: (-1) replace_in_file.Rd:40: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'gofastr-Ex.R' failed
The error most likely occurred in:

> ### Name: as_dtm
> ### Title: Coerce Various Object Into a
> ###   'DocumentTermMatrix'/'TermDocumentMatrix'
> ### Aliases: as_dtm as_tdm
> ### Keywords: documenttermmatrix, termdocumentmatrix
> 
> ### ** Examples
> 
> with(partial_republican_debates_2015,
+     as_dtm(dialogue, paste(location, element_id, sentence_id, sep = "_"))
+ )
Error:
! The `stem` argument of `dfm()` was deprecated in quanteda 3.0 and is
  now defunct.
ℹ Please use `dfm_stem()` instead.
Backtrace:
     ▆
  1. ├─base::with(...)
  2. └─base::with.default(...)
  3.   └─base::eval(substitute(expr), data, enclos = parent.frame())
  4.     └─base::eval(substitute(expr), data, enclos = parent.frame())
  5.       ├─gofastr::as_dtm(...)
  6.       └─gofastr:::as_dtm.character(...)
  7.         ├─tm::weightTfIdf(q_dtm(x, ...))
  8.         └─gofastr::q_dtm(x, ...)
  9.           ├─quanteda::convert(...)
 10.           └─quanteda::dfm(...)
 11.             └─quanteda:::check_defunct_dfm_args(names(as.list(sys.call())[-1]))
 12.               └─lifecycle::deprecate_stop(...)
 13.                 └─lifecycle:::deprecate_stop0(msg)
 14.                   └─rlang::cnd_signal(...)
Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) BVDWSTOXX.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:16: Escaped LaTeX specials: \& \&
checkRd: (-1) BVDWSTOXX.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:37: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R   6.1Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) barplot2.Rd:219: Escaped LaTeX specials: \_
checkRd: (-1) colorpanel.Rd:31: Escaped LaTeX specials: \#
checkRd: (-1) qqnorm.aov.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) venn.Rd:59: Escaped LaTeX specials: \_
Specified C++11: please drop specification unless essential
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    3.5Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
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    help   5.2Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) corrApp.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) crdApp.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) descApp.Rd:55: Escaped LaTeX specials: \&
checkRd: (-1) layoutApp.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) rbdApp.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) ttApp.Rd:43: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    help   2.0Mb
    libs   1.2Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
accrualReport: multiple local function definitions for 'gg' with
  different formal arguments
Package suggested but not available for checking: 'doMC'
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   2.7Mb
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    extdata   5.0Mb
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) fmddisc.Rd:23: Escaped LaTeX specials: \_
checkRd: (-1) schuster.Rd:46: Escaped LaTeX specials: \_
checkRd: (-1) schuster.Rd:54: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    4.1Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 267.7Mb
  sub-directories of 1Mb or more:
    R       1.5Mb
    java  264.7Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
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    doc    1.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.4Mb
  sub-directories of 1Mb or more:
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    shiny   4.3Mb
'LazyData' is specified without a 'data' directory
installed size is  8.1Mb
  sub-directories of 1Mb or more:
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There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.ga.breed' '.ga.fitness' '.ga.init' '.ga.mutate' '.ga.step'
  '.ga.weight'
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    doc    2.6Mb
    libs   1.3Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
GNU make is a SystemRequirements.
Specified C++14: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R         2.6Mb
    extdata   1.3Mb
GNU make is a SystemRequirements.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc           2.7Mb
    htmlwidgets   2.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
Specified C++11: please drop specification unless essential
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   1.4Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    3.7Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.4Mb
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [27s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(httptest2)
  > library(hexFinder)
  > 
  > test_check("hexFinder")
  No github personal access token provided.
  Limited search rates for github will apply.
  Set up github_pat environmental variable if you plan to query multiple repos in a short time
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 33 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-gather.R:13:3'): get_metacran_info ─────────────────────────────
  Error in `open.connection(con, "rb")`: cannot open the connection to 'https://search.r-pkg.org/package/_search?q=Package:notAPackage'
  Backtrace:
       ▆
    1. ├─testthat::expect_null(get_metacran_info("notAPackage")) at test-gather.R:13:3
    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. └─hexFinder:::get_metacran_info("notAPackage")
    5.   └─jsonlite::fromJSON(glue("https://search.r-pkg.org/package/_search?q=Package:{pkg_name}"))
    6.     └─jsonlite:::parse_and_simplify(...)
    7.       └─jsonlite:::parseJSON(txt, bigint_as_char)
    8.         └─jsonlite:::parse_con(txt, bigint_as_char)
    9.           ├─base::open(con, "rb")
   10.           └─base::open.connection(con, "rb")
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 33 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ohio.Rd:104: Escaped LaTeX specials: \&
checkRd: (-1) ohio.Rd:105: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'INLA'
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'colorfulVennPlot'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package which this enhances but not available for checking: 'HadoopStreaming'
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.3Mb
html_describe_con: multiple local function definitions for 'g' with
  different formal arguments
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) disc42.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) discrimination.Rd:31: Escaped LaTeX specials: \&
installed size is 15.0Mb
  sub-directories of 1Mb or more:
    libs  13.8Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'glmmADMB'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    app   1.7Mb
    doc   3.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'RGtk2', 'cairoDevice'
Specified C++11: please drop specification unless essential
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    doc    2.3Mb
    help   1.1Mb
Specified C++14: please drop specification unless essential
checkRd: (-1) simplePostToHost.Rd:14: Escaped LaTeX specials: \&
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'hurricaneexposuredata'
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'microViz'
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
    libs      1.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    extdata   5.8Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   6.3Mb
checkRd: (-1) palettes.Rd:25: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'SparkR'
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    1.6Mb
    libs   1.0Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.1000genomes.hs37d5',
  'BSgenome.Mmusculus.UCSC.mm10'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'icd'
checkRd: (-1) ICEscale.Rd:53: Escaped LaTeX specials: \^
checkRd: (-1) dpwdg.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) dpwdg.Rd:15: Escaped LaTeX specials: \$
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'rggobi'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'IFCdata'
'LazyData' is specified without a 'data' directory
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.2Mb
    help   1.9Mb
    libs   6.3Mb
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    dlib-19.20   9.3Mb
    libs         1.4Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is 20.0Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       3.7Mb
    extdata   1.0Mb
    include   3.0Mb
    libs     10.2Mb
installed size is 21.6Mb
  sub-directories of 1Mb or more:
    libs   10.5Mb
    share  10.2Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    1.6Mb
    libs   1.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'accdata'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) school23.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) school23.Rd:35: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
Package which this enhances but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
Package suggested but not available for checking: 'INLA'
Package suggested but not available for checking: 'INLA'
Package suggested but not available for checking: 'INLA'
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    INSPECTumours (development version)
Malformed Title field: should not end in a period.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    doc   9.9Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
Package unavailable to check Rd xrefs: 'INLA'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'surveyspec'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File 'iotools/libs/x64/iotools.dll':
  Found non-API calls to R: 'R_GetConnection', 'R_ReadConnection',
    'R_WriteConnection'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
checkRd: (-1) constrained.Rd:49: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) bp.coeff.raw.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) bp.coeff.raw.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) bp.coeff.raw.Rd:53: Escaped LaTeX specials: \&
checkRd: (-1) fleiss.kappa.raw.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) landis.koch.bf.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) landis.koch.bf.Rd:17: Escaped LaTeX specials: \&
checkRd: (-1) ir_to_transmittance.Rd:49: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:9: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_loglikelihood.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS2.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS2.model_optimize.kappa.kappa_loglikelihood.Rd:11: Escaped LaTeX specials: \$
Specified C++14: please drop specification unless essential
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    2.3Mb
    libs   3.1Mb
GNU make is a SystemRequirements.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gurobi'
Package suggested but not available for checking: 'locClass'
Packages suggested but not available for checking: 'gurobi', 'cplexAPI'
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    art_profiles   1.5Mb
    libs          11.0Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    htmlwidgets   5.7Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
    libs      1.1Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    R      3.9Mb
    i18n   6.5Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package which this enhances but not available for checking: 'remMap'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    pre-release juicr (2017 - 2021)
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    help   6.6Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'bw.abram.temp':
  'bw.abram.temp'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Minor Changes
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'rkward'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'RGeostats'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'koRpus.lang.de', 'koRpus.lang.es', 'koRpus.lang.fr',
  'koRpus.lang.it', 'koRpus.lang.nl', 'koRpus.lang.pt',
  'koRpus.lang.ru'

Package which this enhances but not available for checking: 'rkward'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   8.2Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   1.7Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) LaplaceApproximation.Rd:485: Escaped LaTeX specials: \&
checkRd: (-1) LossMatrix.Rd:115: Escaped LaTeX specials: \&
checkRd: (-1) LossMatrix.Rd:117: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) LKrig.MLE.Rd:114: Escaped LaTeX specials: \$ \$
checkRd: (-1) LKrig.MLE.Rd:115: Escaped LaTeX specials: \$
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   6.4Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    light.interception.voxels() - This function create the Fraction absorbed incident light
    light.interception.raster() - Create a raster of Fraction absorbed incident light
    light.incident.voxels() - This function create the Fraction incident light
    light.incident.raster() - Create a raster of the Fraction incident light
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
checkRd: (-1) leaps.Rd:38: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   5.5Mb
Package suggested but not available for checking: 'doMC'
GNU make is a SystemRequirements.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   6.0Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs   4.0Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
Specified C++11: please drop specification unless essential
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) hydro.Rd:17: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'rsyslog'
Problems with news in 'NEWS.md':
No news entries found.
Specified C++11: please drop specification unless essential
checkRd: (-1) predict.lb.Rd:16: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R         1.0Mb
    doc       1.0Mb
    extdata   1.1Mb
    libs      1.7Mb
Packages suggested but not available for checking:
  'gWidgets', 'gWidgetsRGtk2', 'RGtk2'
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Running examples in 'locateip-Ex.R' failed
The error most likely occurred in:

> ### Name: locate_ip
> ### Title: Locate an IP adress
> ### Aliases: locate_ip
> 
> ### ** Examples
> 
> locate_ip("132.203.167.188")
Error in `httr2::req_perform()`:
! HTTP 403 Forbidden.
Backtrace:
    ▆
 1. └─locateip::locate_ip("132.203.167.188")
 2.   └─locateip:::get_location(...)
 3.     └─httr2::req_perform(...)
 4.       └─httr2:::handle_resp(req, resp, error_call = error_call)
 5.         └─httr2:::resp_abort(resp, req, body, call = error_call)
 6.           └─rlang::abort(...)
Execution halted
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(locateip)
  > 
  > test_check("locateip")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 8 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-locate.R:32:3'): locate ip works ───────────────────────────────
  <httr2_http_403/httr2_http/httr2_error/rlang_error/error/condition>
  Error in `httr2::req_perform(create_req(ip = ip, fields = fields, lang = lang, 
      header = header, ..., format = format))`: HTTP 403 Forbidden.
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(...) at test-locate.R:32:3
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─locateip::locate_ip("132.203.167.188", tidy = TRUE)
   5.   └─locateip:::get_location(...)
   6.     └─httr2::req_perform(...)
   7.       └─httr2:::handle_resp(req, resp, error_call = error_call)
   8.         └─httr2:::resp_abort(resp, req, body, call = error_call)
   9.           └─rlang::abort(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 8 ]
  Error: Test failures
  Execution halted
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    Bug Fixes
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Running examples in 'mlr3spatiotempcv-Ex.R' failed
The error most likely occurred in:

> ### Name: mlr_resamplings_repeated_spcv_knndm
> ### Title: (CAST) Repeated K-fold Nearest Neighbour Distance Matching
> ### Aliases: mlr_resamplings_repeated_spcv_knndm
> ###   ResamplingRepeatedSpCVKnndm
> 
> ### ** Examples
> 
> library(mlr3)
> library(mlr3spatial)

Attaching package: 'mlr3spatial'

The following objects are masked from 'package:mlr3spatiotempcv':

    TaskClassifST, TaskRegrST, as_task_classif_st,
    as_task_classif_st.DataBackend, as_task_classif_st.TaskClassifST,
    as_task_classif_st.data.frame, as_task_classif_st.sf,
    as_task_regr_st, as_task_regr_st.DataBackend,
    as_task_regr_st.TaskClassifST, as_task_regr_st.TaskRegrST,
    as_task_regr_st.data.frame, as_task_regr_st.sf

> set.seed(42)
> simarea = list(matrix(c(0, 0, 0, 100, 100, 100, 100, 0, 0, 0), ncol = 2, byrow = TRUE))
> simarea = sf::st_polygon(simarea)
> train_points = sf::st_sample(simarea, 1000, type = "random")
> train_points = sf::st_as_sf(train_points)
> train_points$target = as.factor(sample(c("TRUE", "FALSE"), 1000, replace = TRUE))
> pred_points = sf::st_sample(simarea, 1000, type = "regular")
> 
> task = mlr3spatial::as_task_classif_st(sf::st_as_sf(train_points), "target", positive = "TRUE")
> 
> cv_knndm = rsmp("repeated_spcv_knndm", ppoints = pred_points, repeats = 2)
> cv_knndm$instantiate(task)
Error in CAST::knndm(tpoints = points, modeldomain = self$param_set$values$modeldomain,  : 
  unused argument (ppoints = self$param_set$values$ppoints)
Calls: <Anonymous> ... .__ResamplingRepeatedSpCVKnndm__.sample -> map -> lapply -> FUN
Execution halted
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S3 methods shown with full name in documentation object 'pamr-internal':
  'print.nsc' 'print.nsccv'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
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Found the following significant warnings:
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See 'd:/Rcompile/CRANpkg/local/4.3/pcaL1.Rcheck/00install.out' for details.
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Package suggested but not available for checking: 'gurobi'
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc       1.7Mb
    extdata   4.1Mb
    libs      1.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    libs   1.4Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'cairoDevice', 'RGtk2'
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    etc    1.9Mb
    po     1.2Mb
checkRd: (-1) acquireAuditData.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) rattle.Rd:44: Escaped LaTeX specials: \_
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   1.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    libs   1.2Mb
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rrelaxiv'
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'rrelaxiv'
'LazyData' is specified without a 'data' directory
installed size is 20.2Mb
  sub-directories of 1Mb or more:
    cont  20.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Depends: includes the non-default packages:
  'biclust', 'fabia', 'iBBiG', 'superbiclust', 'BcDiag', 'BicARE',
  's4vd', 'BiBitR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'LazyData' is specified without a 'data' directory
checkRd: (-1) RcmdrPlugin.MA-package.Rd:21: Escaped LaTeX specials: \&
checkRd: (-1) RcmdrPlugin.MA-package.Rd:23: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'ROpenOffice'
Depends: includes the non-default packages:
  'IQCC', 'qcc', 'qicharts2', 'randtests', 'rmarkdown',
  'TeachingDemos', 'tseries'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   3.5Mb
    po    2.4Mb
Package suggested but not available for checking: 'conics'
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    corpora   7.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/Rcplex.Rcheck/00install.out' for details.
Specified C++11: please drop specification unless essential
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    include   6.6Mb
    libs      1.2Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
installed size is 46.7Mb
  sub-directories of 1Mb or more:
    include  46.4Mb
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    include   9.6Mb
    libs      1.2Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    include   6.4Mb
    libs      1.1Mb
GNU make is a SystemRequirements.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    include   6.4Mb
    libs      1.3Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    include        2.0Mb
    jsonexamples   3.8Mb
    libs           2.0Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   2.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'rdss-Ex.R' failed
The error most likely occurred in:

> ### Name: process_tracing_estimator
> ### Title: Process tracing estimator
> ### Aliases: process_tracing_estimator
> 
> ### ** Examples
> 
> # Simple example showing ambiguity in attribution
> process_tracing_estimator(
+   causal_model = CausalQueries::make_model("X -> Y"),
+   query = "Y[X=1] > Y[X=0]",
+   data = data.frame(X=1, Y = 1),
+   strategies = "X-Y")
Loading required namespace: CausalQueries
Error in `dplyr::select()`:
! Can't select columns that don't exist.
✖ Column `sd` doesn't exist.
Backtrace:
     ▆
  1. ├─base (local) `<fn>`(x)
  2. ├─CausalQueries:::print.model_query(x)
  3. │ ├─dplyr::select(x, -sd, -cred.low, -cred.high)
  4. │ └─dplyr:::select.data.frame(x, -sd, -cred.low, -cred.high)
  5. │   └─tidyselect::eval_select(expr(c(...)), data = .data, error_call = error_call)
  6. │     └─tidyselect:::eval_select_impl(...)
  7. │       ├─tidyselect:::with_subscript_errors(...)
  8. │       │ └─base::withCallingHandlers(...)
  9. │       └─tidyselect:::vars_select_eval(...)
 10. │         └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
 11. │           └─tidyselect:::eval_c(expr, data_mask, context_mask)
 12. │             └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
 13. │               └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
 14. │                 └─tidyselect:::as_indices_sel_impl(...)
 15. │                   └─tidyselect:::as_indices_impl(...)
 16. │                     └─tidyselect:::chr_as_locations(x, vars, call = call, arg = arg)
 17. │                       └─vctrs::vec_as_location(...)
 18. └─vctrs (local) `<fn>`()
 19.   └─vctrs:::stop_subscript_oob(...)
 20.     └─vctrs:::stop_subscript(...)
 21.       └─rlang::abort(...)
Execution halted
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    data   1.5Mb
Package suggested but not available for checking: 'dataui'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    htmlwidgets   9.8Mb
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   9.0Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   2.0Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    include   6.5Mb
    libs      1.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'Rcplex'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    libs   1.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   1.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) cast.Rd:45: Escaped LaTeX specials: \_
checkRd: (-1) cast.Rd:46: Escaped LaTeX specials: \_
checkRd: (-1) as-data-frame-cast-df-v7.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) as-data-frame-cast-matrix-59.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) as-matrix-cast-df-bu.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) as-matrix-cast-matrix-2y.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) cast-9g.rd:19: Escaped LaTeX specials: \_ \_
checkRd: (-1) cast-9g.rd:41: Escaped LaTeX specials: \_
checkRd: (-1) cast-9g.rd:46: Escaped LaTeX specials: \_ \_
checkRd: (-1) clean-vars-rc.rd:13: Escaped LaTeX specials: \_
checkRd: (-1) expand-kx.rd:15: Escaped LaTeX specials: \_
checkRd: (-1) reshape-4u.rd:17: Escaped LaTeX specials: \_ \_
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   1.3Mb
    java      2.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    libs      1.7Mb
    models    1.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    examples   1.9Mb
checkRd: (-1) rec.Rd:23: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/revert.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Problems with news in 'NEWS.md':
No news entries found.
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    data  13.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data      1.9Mb
    doc       1.2Mb
    extdata   1.9Mb
Problems with news in 'NEWS.md':
No news entries found.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    doc     3.0Mb
    fonts   1.5Mb
    libs    2.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    doc          10.3Mb
    htmlwidgets   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'mimic.demo', 'eicu.demo'
Specified C++11: please drop specification unless essential
checkRd: (-1) acg.Rd:72: Escaped LaTeX specials: \&
checkRd: (-1) gorilla.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) grassmann.utest.Rd:63: Escaped LaTeX specials: \&
checkRd: (-1) macg.Rd:71: Escaped LaTeX specials: \&
checkRd: (-1) sphere.utest.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) stiefel.utest.Rd:64: Escaped LaTeX specials: \&
checkRd: (-1) wrap.landmark.Rd:41: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    lib    3.3Mb
    libs   4.1Mb
File 'RInside/libs/x64/RInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/x64/libRInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/x64/RInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLinit', 'R_RunExitFinalizers', 'R_SetParams', 'R_TempDir',
    'Rf_endEmbeddedR', 'Rf_initEmbeddedR', 'getRUser', 'get_R_HOME',
    'run_Rmainloop'
File 'RInside/libs/x64/libRInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLinit', 'R_RunExitFinalizers', 'R_SetParams', 'R_TempDir',
    'Rf_endEmbeddedR', 'Rf_initEmbeddedR', 'getRUser', 'get_R_HOME',
    'run_Rmainloop'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf.
Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following possibly unsafe calls:
File 'rJava/R/import.R':
  unlockBinding(IMPORTER, env = env)
  assignInNamespace(IMPORTER, importer, envir = env)
File 'rJava/R/jinit.R':
  unlockBinding(x, .env)
  unlockBinding(x, pe)
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  jri/src/Makefile.win
  jri/src/win32/Makefile
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/4.3/rJava/libs/x64/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    java   4.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    include   3.1Mb
    libs      2.4Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.0Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.8Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    datasets  10.2Mb
installed size is 50.2Mb
  sub-directories of 1Mb or more:
    R     4.0Mb
    exe  45.7Mb
'LazyData' is specified without a 'data' directory
installed size is 24.6Mb
  sub-directories of 1Mb or more:
    extdata  23.8Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) Exponential.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) Gamma.Rd:80: Escaped LaTeX specials: \&
checkRd: (-1) college.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) college.Rd:15: Escaped LaTeX specials: \$
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    lemon   2.9Mb
    libs    2.1Mb
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
GNU make is a SystemRequirements.
installed size is 33.7Mb
  sub-directories of 1Mb or more:
    hdf5     16.0Mb
    include   6.5Mb
    lib       2.6Mb
    libs      8.2Mb
GNU make is a SystemRequirements.
Packages suggested but not available for checking:
  'DoubletFinder', 'RcppPlanc'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    rmd   5.9Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) cGARCHfilter-class.Rd:57: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHfit-class.Rd:59: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHsim-class.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHspec-class.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) cgarchsim-methods.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) goGARCHfilter-class.Rd:155: Escaped LaTeX specials: \&
checkRd: (-1) goGARCHfit-class.Rd:166: Escaped LaTeX specials: \&
checkRd: (-1) rmgarch-package.Rd:73: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs       1.0Mb
    minizinc   2.3Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
Package unavailable to check Rd xrefs: 'cmdstanr'
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
GNU make is a SystemRequirements.
Error(s) in re-building vignettes:
--- re-building 'rnaCrosslinkOO.Rmd' using rmarkdown
File rnaCrosslinkProtocol.jpg not found in resource path
Error: processing vignette 'rnaCrosslinkOO.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'rnaCrosslinkOO.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    doc    2.2Mb
Package suggested but not available for checking: 'rnaturalearthhires'
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.1Mb
Malformed Title field: should not end in a period.
checkRd: (-1) NlistServersInCategory.Rd:11: Escaped LaTeX specials: \_
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    libs  15.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      3.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    doc    1.7Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    R  11.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/RobLoxBioC.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  d:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.3.0\include\emmintrin.h:134:24: warning: array subscript '__m128d_u[0]' is partly outside array bounds of 'Eigen::internal::plain_matrix_type<Eigen::Product<Eigen::Block<Eigen::Matrix<double, -1, -1>, 1, -1, false>, Eigen::Transpose<Eigen::Block<Eigen::Matrix<double, -1, -1>, 1, -1, false> >, 0>, Eigen::Dense>::type [1]' {aka 'Eigen::Matrix<double, 1, 1, 0, 1, 1> [1]'} [-Warray-bounds]
See 'd:/Rcompile/CRANpkg/local/4.3/RobustGaSP.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
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    libs              1.3Mb
    simulationStudy   1.6Mb
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) performance.Rd:35: Escaped LaTeX specials: \#
checkRd: (-1) performance.Rd:36: Escaped LaTeX specials: \# \# \#
checkRd: (-1) performance.Rd:37: Escaped LaTeX specials: \# \#
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package required but not available: 'Rcplex'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    doc  15.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R         2.7Mb
    extdata   2.7Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/ROracle.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   2.7Mb
    libs   1.5Mb
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      4.2Mb
    libs   1.6Mb
Package suggested but not available for checking: 'RandomFields'
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   1.4Mb
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   3.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    libs  16.3Mb
GNU make is a SystemRequirements.
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/4.3/Rserve/libs/x64/Rserve.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'Rserve/libs/x64/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'R_Visible',
    'Rf_initialize_R', 'setup_Rmainloop'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gurobi'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 18.9Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
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    lib    2.0Mb
    libs   1.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    libs   2.3Mb
Specified C++11: please drop specification unless essential
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    libs  18.6Mb
installed size is 41.6Mb
  sub-directories of 1Mb or more:
    libs    1.1Mb
    swipl  40.4Mb
GNU make is a SystemRequirements.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.4Mb
    help   2.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    rmarkdown  11.0Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R   5.0Mb
Specified C++11: please drop specification unless essential
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs   2.5Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'cmdstanr'
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   9.9Mb
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   1.1Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   1.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'glmmADMB'
'LazyData' is specified without a 'data' directory
Running 'spelling.R' [0s]
  Running 'testthat.R' [23s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(rvest)
  > 
  > test_check("rvest")
  Starting 2 test processes
  [ FAIL 1 | WARN 0 | SKIP 42 | PASS 103 ]
  
  ══ Skipped tests (42) ══════════════════════════════════════════════════════════
  • On CRAN (40): 'test-html.R:16:3', 'test-live.R:2:3', 'test-live.R:9:3',
    'test-live.R:26:3', 'test-live.R:34:3', 'test-live.R:43:3',
    'test-live.R:54:3', 'test-live.R:73:3', 'test-live.R:81:3',
    'test-live.R:95:3', 'test-form.R:29:3', 'test-form.R:76:3',
    'test-form.R:85:3', 'test-form.R:107:3', 'test-form.R:119:3',
    'test-form.R:144:3', 'test-form.R:177:3', 'test-form.R:215:3',
    'test-selectors.R:63:3', 'test-rename.R:4:3', 'test-rename.R:21:3',
    'test-rename.R:25:3', 'test-table.R:11:3', 'test-table.R:40:3',
    'test-table.R:55:3', 'test-table.R:69:3', 'test-table.R:84:3',
    'test-table.R:100:3', 'test-table.R:115:3', 'test-table.R:128:3',
    'test-table.R:175:3', 'test-table.R:186:3', 'test-table.R:196:3',
    'test-table.R:202:3', 'test-table.R:208:3', 'test-utils.R:7:3',
    'test-session.R:22:3', 'test-session.R:43:3', 'test-session.R:53:3',
    'test-session.R:82:3'
  • currently broken (2): 'test-encoding.R:2:3', 'test-encoding.R:14:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-session.R:2:3'): basic session process works as expected ───────
  Error in `curl::curl_fetch_memory(url, handle = handle)`: Empty reply from server
  Backtrace:
      ▆
   1. └─testthat::expect_snapshot(...) at test-session.R:2:3
   2.   └─rlang::cnd_signal(state$error)
  
  [ FAIL 1 | WARN 0 | SKIP 42 | PASS 103 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: 'gpuR'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    include   5.2Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    include   5.0Mb
    libs      5.2Mb
Problems with news in 'NEWS.md':
No news entries found.
S3 methods shown with full name in documentation object 'matmult':
  '%*%.rv'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rWCVPdata'
Specified C++11: please drop specification unless essential
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
'LazyData' is specified without a 'data' directory
File 'RWinEdt/R/zzz.R':
  .onAttach calls:
    writeLines(edtFile, con = send2RedtLoc)
    writeLines(edtFile, con = send2RedtLoc)

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    3.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   2.6Mb
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'unix'
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
matrixOps:
  function(x, y)
matrixOps.S7_object:
  function(e1, e2)
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
checkRd: (-1) BootsChapt.Rd:38: Escaped LaTeX specials: \&
checkRd: (-1) SemiparChangePoint.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) schapt.Rd:44: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) SAM.Rd:67: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:59: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:84: Escaped LaTeX specials: \# \$
checkRd: (-1) samr.Rd:88: Escaped LaTeX specials: \$
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checkRd: (-1) samr.Rd:97: Escaped LaTeX specials: \#
checkRd: (-1) samr.assess.samplesize.plot.Rd:12: Escaped LaTeX specials: \#
installed size is 15.4Mb
  sub-directories of 1Mb or more:
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    libs  13.5Mb
Specified C++11: please drop specification unless essential
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.4Mb
    libs   1.3Mb
Package suggested but not available for checking: 'networkTomography'
'sandwich-CL.Rnw'... [12s] NOTE
differences from 'sandwich-CL.Rout.save'
82c82
< Classes and Methods for R originally developed in the
---
> Classes and Methods for R developed in the
85,87c85,87
< Stanford University (2002-2015),
< by and under the direction of Simon Jackman.
< hurdle and zeroinfl functions by Achim Zeileis.
---
> Stanford University
> Simon Jackman
> hurdle and zeroinfl functions by Achim Zeileis
  'sandwich-OOP.Rnw'... [3s] OK
  'sandwich.Rnw'... [1s] OK
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    bin   5.8Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
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    libs   3.0Mb
GNU make is a SystemRequirements.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc       5.1Mb
    extdata   1.2Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
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    libs   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Updated help pages with examples
    Updated conjugate model sampler
Specified C++11: please drop specification unless essential
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex', 'pogs'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) x.oreo.Rd:48: Escaped LaTeX specials: \_ \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'sceasy', 'SeuratDisk', 'SeuratWrappers'
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) simulateSNPs.Rd:46: Escaped LaTeX specials: \& \& \&
checkRd: (-1) simulateSNPs.Rd:80: Escaped LaTeX specials: \& \& \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    R   8.1Mb
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    extdata  18.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    libs   2.0Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 34.5Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.0Mb
  sub-directories of 1Mb or more:
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    models   1.6Mb
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    6.4Mb
    libs   1.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
Package suggested but not available for checking: 'doMC'
GNU make is a SystemRequirements.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs   1.0Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) SEset_to_network.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) network_to_SEset.Rd:72: Escaped LaTeX specials: \&
checkRd: (-1) network_to_path.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) path_to_network.Rd:29: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'BPCells'
Packages suggested but not available for checking: 'BPCells', 'presto'
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    doc   4.9Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
installed size is 107.4Mb
  sub-directories of 1Mb or more:
    doc      1.7Mb
    gdal     3.0Mb
    libs    89.7Mb
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    sqlite   1.5Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
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installed size is  6.4Mb
  sub-directories of 1Mb or more:
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    doc   3.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rCOSA'
Package unavailable to check Rd xrefs: 'rCOSA'
Package suggested but not available for checking: 'hydromad'
installed size is  6.3Mb
  sub-directories of 1Mb or more:
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    extdata   4.2Mb
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
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Package suggested but not available for checking: 'cmdstanr'
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'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 21.1Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
installed size is 12.8Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.7Mb
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Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/SIGN.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    simpleCache [0.0.1]
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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Package suggested but not available for checking: 'INLA'
Specified C++14: please drop specification unless essential
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Version (Date)
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
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Error(s) in re-building vignettes:
--- re-building 'vignette_simple_usage.Rmd' using knitr

Quitting from lines  at lines 7-14 [unnamed-chunk-1] (vignette_simple_usage.Rmd)
Error: processing vignette 'vignette_simple_usage.Rmd' failed with diagnostics:
cannot open the connection to 'https://seafile.utu.fi/f/13e0ef294b374549b499/?dl=1'
--- failed re-building 'vignette_simple_usage.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package which this enhances but not available for checking: 'kmndirs'
Unavailable namespace imported from by a ':::' call: 'kmndirs'
  See the note in ?`:::` about the use of this operator.
GNU make is a SystemRequirements.
installed size is  5.5Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
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installed size is  5.9Mb
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Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) slp-package.Rd:38: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gurobi'
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
checkRd: (-1) customerRetentionDemographics.Rd:10: Escaped LaTeX specials: \$
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Package suggested but not available for checking: 'doMC'
installed size is  6.7Mb
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'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
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'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
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checkRd: (-1) llwrPTF.Rd:7: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
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installed size is  5.5Mb
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checkRd: (-1) plot.som.Rd:27: Escaped LaTeX specials: \_
checkRd: (-1) som.Rd:128: Escaped LaTeX specials: \_
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Package suggested but not available for checking: 'SciencesPo'
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
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Package suggested but not available for checking: 'gridlayout'
installed size is  5.9Mb
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'NLMR'
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is 13.5Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
installed size is 14.6Mb
  sub-directories of 1Mb or more:
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Specified C++11: please drop specification unless essential
installed size is  5.4Mb
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Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Depends: includes the non-default packages:
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Adding so many packages to the search path is excessive and importing
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Depends: includes the non-default packages:
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Adding so many packages to the search path is excessive and importing
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Depends: includes the non-default packages:
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Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
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Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
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Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is  5.4Mb
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'spDataLarge'
installed size is  6.5Mb
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installed size is  5.9Mb
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installed size is  8.1Mb
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Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Roadmap of specklestar package
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
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checkRd: (-1) image.plot.Rd:78: Escaped LaTeX specials: \$
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Feature Changes
Specified C++11: please drop specification unless essential
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Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
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Specified C++11: please drop specification unless essential
checkRd: (-1) shypEstFun.Rd:52: Escaped LaTeX specials: \$
checkRd: (-1) shypEstFun.Rd:54: Escaped LaTeX specials: \$
installed size is  7.0Mb
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installed size is  5.1Mb
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'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.7Mb
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installed size is  5.4Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.4Mb
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'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  5.5Mb
  sub-directories of 1Mb or more:
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installed size is  6.9Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 14.1Mb
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GNU make is a SystemRequirements.
installed size is  6.0Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'starsdata'
installed size is  6.3Mb
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checkRd: (-1) multiCUMSUM.Rd:33: Escaped LaTeX specials: \&
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Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: 'asreml'
Package suggested but not available for checking: 'asreml'
Package suggested but not available for checking: 'asreml'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following possibly unsafe calls:
File 'statnet.common/R/control.utilities.R':
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  unlockBinding("snctrl", environment(update_my_snctrl))
Package suggested but not available for checking: 'networksis'
unable to reach CRAN

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
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checkRd: (-1) stdGlm.Rd:93: Escaped LaTeX specials: \&
installed size is 14.6Mb
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Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  6.8Mb
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installed size is 14.3Mb
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Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Package suggested but not available for checking: 'StrathE2E2examples'
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
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Malformed Title field: should not end in a period.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 35.4Mb
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installed size is  9.1Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'STRaitRazoR'
efpFunctional: multiple local function definitions for 'plotProcess'
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mefp.efp: multiple local function definitions for 'computeEmpProc' with
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checkRd: (-1) SP2001.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) SP2001.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) SP2001.Rd:12: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
installed size is  5.9Mb
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Package suggested but not available for checking: 'extraTrees'
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Specified C++11: please drop specification unless essential
surfaceSimulate : phytransform: no visible global function definition
  for 'rescale'
Undefined global functions or variables:
  rescale
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
installed size is  7.4Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
installed size is  5.9Mb
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Package suggested but not available for checking: 'gurobi'
Packages suggested but not available for checking:
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installed size is  8.1Mb
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Specified C++11: please drop specification unless essential
installed size is  6.0Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'swephRdata'
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Additional functions and data sets
    Amendments to functions
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    pre-release switchboard (2020 - 2021)
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'sylly.de', 'sylly.es'
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
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Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
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    doc    1.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'unix'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R         1.3Mb
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Specified C++11: please drop specification unless essential
installed size is  6.0Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
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checkRd: (-1) tmCtypes.Rd:22: Escaped LaTeX specials: \#
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Specified C++11: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) tapnet-package.Rd:40: Escaped LaTeX specials: \&
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Package suggested but not available for checking: 'tashudata'
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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installed size is 13.5Mb
  sub-directories of 1Mb or more:
    doc  12.3Mb
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    7.5Mb
    libs   1.1Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc    4.5Mb
    help   2.7Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 107.5Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    gdal   3.0Mb
    libs  92.5Mb
    proj   8.4Mb
installed size is 23.3Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       8.1Mb
    tessdata  14.0Mb
Package suggested but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages which this enhances but not available for checking:
  'mnlogit', 'Zelig'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    rda    7.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      4.1Mb
    data   3.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) CPdimensionalityplot.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) CPdimensionalityplot.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) Kinship.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) Kinship.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) T2func.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) T2funcrep.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) T3dimensionalityplot.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) T3func.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) T3func.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) T3funcrep.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) T3funcrep.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:26: Escaped LaTeX specials: \& \& \&
checkRd: (-1) TV.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) pcamean.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) threewayanova.Rd:24: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Initial Release (v0.1.0)
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Minor changes:
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc       2.0Mb
    extdata   4.5Mb
Package suggested but not available for checking: 'rrelaxiv'
installed size is 22.8Mb
  sub-directories of 1Mb or more:
    libs  20.5Mb
checkRd: (-1) compare.Rd:46: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   3.0Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  D:/RCompile/recent/R-4.3.2/Tcl/include/X11/Xlib.h:131:9: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R-4.3.2/Tcl/include/X11/Xlib.h:334:16: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R-4.3.2/Tcl/include/X11/Xlib.h:453:9: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R-4.3.2/Tcl/include/X11/Xlib.h:471:9: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R-4.3.2/Tcl/include/X11/Xlib.h:496:9: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R-4.3.2/Tcl/include/X11/Xlib.h:497:9: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R-4.3.2/Tcl/include/X11/Xlib.h:509:9: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R-4.3.2/Tcl/include/X11/Xlib.h:522:9: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R-4.3.2/Tcl/include/X11/Xlib.h:1053:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  tcltkimg.c:93:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  tcltkimg.c:94:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
See 'd:/Rcompile/CRANpkg/local/4.3/tkrplot.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    examples  12.7Mb
    include    3.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Rcampdf', 'Rpoppler', 'tm.lexicon.GeneralInquirer'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data-tables   1.4Mb
    doc           1.9Mb
    help          1.2Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'RGtk2', 'gWidgets2RGtk2'
Package suggested but not available for checking: 'gurobi'
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
installed size is 26.9Mb
  sub-directories of 1Mb or more:
    R         5.6Mb
    help      1.6Mb
    include   1.8Mb
    libs     17.4Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'toscaData'
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    data  12.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    2.8Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'taxidata'
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  13.4Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Packages which this enhances but not available for checking:
  'fwelnet', 'doMC'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Eunomia', 'CohortGenerator', 'CirceR', 'Capr'
checkRd: (-1) dcc.Rd:227: Escaped LaTeX specials: \&
checkRd: (-1) seascorr.Rd:128: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'TreeDistData'
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    5.0Mb
    libs   1.2Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    datasets   1.6Mb
    doc        1.3Mb
    libs       1.1Mb
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    data      1.3Mb
    doc       1.3Mb
    extdata  14.8Mb
Problems with news in 'NEWS.md':
No news entries found.
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   7.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'rrelaxiv', 'gurobi'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Changes
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'log2console'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) TempDisaggDGP.Rd:79: Escaped LaTeX specials: \&
checkRd: (-1) disaggregate.Rd:56: Escaped LaTeX specials: \&
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    libs  13.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   1.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'sl3'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Problems with news in 'NEWS.md':
No news entries found.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc     4.5Mb
    ubinc   2.0Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.0Mb
    libs   4.5Mb
GNU make is a SystemRequirements.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data       1.1Mb
    doc        1.4Mb
    shinyapp   4.9Mb
Specified C++11: please drop specification unless essential
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc         1.4Mb
    dummydata   1.4Mb
    libs        2.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    uktrans_get is fixed when start_date is used (#2)
    Extra layer of of NULL returns to fail gracefully with an informative message.
    Removed travis & appveyor and using gh_actions instead.
    Using gh-pages to create the pkgdown website.
    Create an app as vignette page to search with the help of uklr.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    help   4.4Mb
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 18.5Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.4Mb
    libs  14.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   7.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'USA.state.boundaries.data'
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   3.8Mb
checkRd: (-1) aosat.Rd:20: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) aosat.Rd:21: Escaped LaTeX specials: \_
checkRd: (-1) arctic.oscillations.Rd:19: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) arctic.oscillations.Rd:20: Escaped LaTeX specials: \_
checkRd: (-1) babies.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) babies.Rd:41: Escaped LaTeX specials: \$
checkRd: (-1) cabinet.Rd:25: Escaped LaTeX specials: \$
checkRd: (-1) cabinet.Rd:43: Escaped LaTeX specials: \$
checkRd: (-1) cabinet.Rd:48: Escaped LaTeX specials: \$
checkRd: (-1) exec.pay.Rd:5: Escaped LaTeX specials: \$
checkRd: (-1) sp500.excess.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) sp500.excess.Rd:6: Escaped LaTeX specials: \&
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  randutils.c:60:12: warning: function declaration isn't a prototype [-Wstrict-prototypes]
See 'd:/Rcompile/CRANpkg/local/4.3/uuid.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  22.0Mb
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'vaers', 'vaersND'
Packages suggested but not available for checking: 'vaers', 'vaersND'
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    extdata   8.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 104.4Mb
  sub-directories of 1Mb or more:
    extdata   2.8Mb
    gdal      3.0Mb
    libs     88.9Mb
    proj      8.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) randomVarImpsRFplot.Rd:97: Escaped LaTeX specials: \&
checkRd: (-1) varSelImpSpecRF.Rd:83: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs  10.6Mb
GNU make is a SystemRequirements.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc   7.4Mb
Running 'test-all.R' [12s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library("testthat")
  > library('vcr')
  > test_check("vcr")
  https://hb.opencpu.org is down Timeout was reached: [hb.opencpu.org] Connection timed out after 5014 milliseconds
  https://nghttp2.org/httpbin is down Timeout was reached: [nghttp2.org] Connection timed out after 5012 milliseconds
  Error in `FUN()`:
  ! In path: "D:\\RCompile\\CRANpkg\\local\\4.3\\vcr.Rcheck\\tests\\testthat\\helper-vcr.R"
  Caused by error:
  ! all httpbin servers down
  Backtrace:
       ▆
    1. ├─testthat::test_check("vcr")
    2. │ └─testthat::test_dir(...)
    3. │   └─testthat:::test_files(...)
    4. │     └─testthat:::test_files_serial(...)
    5. │       └─testthat:::test_files_setup_state(...)
    6. │         └─testthat::source_test_helpers(".", env)
    7. │           └─testthat::source_dir(path, "^helper.*\\.[rR]$", env = env, wrap = FALSE)
    8. │             └─base::lapply(...)
    9. │               └─testthat (local) FUN(X[[i]], ...)
   10. │                 └─testthat::source_file(path, env = env, chdir = chdir, wrap = wrap)
   11. │                   ├─base::withCallingHandlers(...)
   12. │                   └─base::eval(exprs, env)
   13. │                     └─base::eval(exprs, env)
   14. │                       └─base::stop("all httpbin servers down") at D:\RCompile\CRANpkg\local\4.3\vcr.Rcheck\tests\testthat\helper-vcr.R:83:1
   15. └─base::.handleSimpleError(...)
   16.   └─testthat (local) h(simpleError(msg, call))
   17.     └─rlang::abort(...)
  Execution halted
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'vdg.Rnw' using knitr

Quitting from lines  at lines 239-244 [spv-example] (vdg.Rnw)
Error: processing vignette 'vdg.Rnw' failed with diagnostics:
there is no package called 'tinytex'
--- failed re-building 'vdg.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) value.Rd:32: Escaped LaTeX specials: \$ \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ex121.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex124.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex125.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex127.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex32.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex33.Rd:18: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R      4.2Mb
    help   3.0Mb
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   5.2Mb
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    help          1.3Mb
    htmlwidgets   5.2Mb
Problems with news in 'NEWS.md':
No news entries found.
GNU make is a SystemRequirements.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    doc           2.0Mb
    htmlwidgets   6.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc       5.4Mb
    extdata   1.1Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'INLA'
Package unavailable to check Rd xrefs: 'INLA'
installed size is 21.8Mb
  sub-directories of 1Mb or more:
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    libs     19.9Mb
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    vortexRdata pre-1.0.3
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) compute.means.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) norm.wattfabricius.Rd:5: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    extdata   8.5Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
'LazyData' is specified without a 'data' directory
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    6.3Mb
    libs   1.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'prepr'
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    client   9.1Mb
    doc      1.0Mb
Packages suggested but not available for checking: 'iptools', 'rgeolocate'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'QIC.gee':
  'QIC.gee'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Major changes
    Minor changes
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Warning in initDict() :
  cannot find WordNet 'dict' directory: please set the environment variable WNHOME to its parent

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   6.5Mb
Malformed Description field: should contain one or more complete sentences.
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    data  12.6Mb
Malformed Description field: should contain one or more complete sentences.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    data  11.1Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
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installed size is 11.2Mb
  sub-directories of 1Mb or more:
    data  11.1Mb
Malformed Title field: should not end in a period.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc       3.5Mb
    extdata   2.5Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    help   1.9Mb
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Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    bin   5.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 27.9Mb
  sub-directories of 1Mb or more:
    java  25.4Mb
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    exampleData   1.3Mb
    libs          2.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'RNRCS', 'metScanR'
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) ZIClass.Rd:87: Escaped LaTeX specials: \_
checkRd: (-1) ZITrain.Rd:72: Escaped LaTeX specials: \_
checkRd: (-1) ZITrain.Rd:74: Escaped LaTeX specials: \_
checkRd: (-1) zid.Rd:45: Escaped LaTeX specials: \_
checkRd: (-1) zim.Rd:63: Escaped LaTeX specials: \_
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 31.1Mb
  sub-directories of 1Mb or more:
    libs  30.7Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    libs   2.5Mb
'LazyData' is specified without a 'data' directory
installed size is 88.8Mb
  sub-directories of 1Mb or more:
    libs  87.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    include  13.4Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    htmlwidgets  11.6Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   5.7Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘hunspell’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    R  14.1Mb
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘RcppProgress’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc   7.1Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs  11.6Mb
File ‘adbcsqlite/libs/adbcsqlite.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
    Object: ‘c/vendor/sqlite3/sqlite3.o’
  Found ‘_random’, possibly from ‘random’ (C)
    Object: ‘c/vendor/sqlite3/sqlite3.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Benchmarking’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   3.0Mb
    libs   2.6Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R       2.1Mb
    data    1.3Mb
    files   1.7Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   2.7Mb
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    data  10.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
Package suggested but not available for checking: ‘HiTC’
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘fields’ ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    tutorials   5.5Mb
Namespaces in Imports field not imported from:
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  ‘effsize’ ‘forcats’ ‘ggplot2’ ‘lm.beta’ ‘nlme’ ‘readr’ ‘robust’
  ‘sandwich’ ‘sjstats’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘cnmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DBI’ ‘assertthat’ ‘tibble’
  All declared Imports should be used.
installed size is  5.7Mb
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installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   3.4Mb
    libs      2.1Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Package which this enhances but not available for checking: ‘asreml’
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
Namespaces in Imports field not imported from:
  ‘devtools’ ‘mixexp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘knitr’ ‘randomNames’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
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    libs   4.1Mb
Namespaces in Imports field not imported from:
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  ‘utils’
  All declared Imports should be used.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
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    doc       3.5Mb
'LazyData' is specified without a 'data' directory
Note: found 710 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following apparent S3 methods exported but not registered:
  print.amAlleleFreq print.amDataset
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    libs  17.7Mb
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [9s/10s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
      ▆
   1. └─altdoc::render_docs(path = getwd()) at test-update.R:111:5
   2.   └─cli::cli_abort("There were some failures when rendering vignettes.")
   3.     └─rlang::abort(...)
  ── Error ('test-update.R:111:5'): render_docs also transform new/modified vignettes if specified: docsify ──
  Error in `render_docs(path = getwd())`: There were some failures when rendering vignettes.
  Backtrace:
      ▆
   1. └─altdoc::render_docs(path = getwd()) at test-update.R:111:5
   2.   └─cli::cli_abort("There were some failures when rendering vignettes.")
   3.     └─rlang::abort(...)
  
  [ FAIL 5 | WARN 0 | SKIP 7 | PASS 56 ]
  Error: Test failures
  Execution halted
Note: found 171 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘metaboliteIDmapping’
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   3.9Mb
'LazyData' is specified without a 'data' directory
Note: found 7 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘devtools’ ‘dplyr’ ‘gridExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘kernlab’
  All declared Imports should be used.
installed size is 25.9Mb
  sub-directories of 1Mb or more:
    libs  24.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 31.7Mb
  sub-directories of 1Mb or more:
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    libs    30.2Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘car’ ‘datasets’ ‘dplyr’ ‘ggplot2’ ‘plotly’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DescTools’ ‘HH’ ‘datasets’ ‘dplyr’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DescTools’ ‘HH’ ‘datasets’ ‘dplyr’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 36.1Mb
  sub-directories of 1Mb or more:
    R  36.1Mb
Package suggested but not available for checking: ‘rhdf5’
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘mcclust’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘curl’ ‘httr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Error: package or namespace load failed for ‘ao’:
 .onLoad failed in loadNamespace() for 'showtext', details:
  call: sysfonts::font_add("wqy-microhei", out_file)
  error: freetype: unknown file format, error code 2
In addition: Warning message:
In utils::unzip(font_file, exdir = out_dir, overwrite = FALSE) :
  write error in extracting from zip file
Execution halted
Error: .onLoad failed in loadNamespace() for 'showtext', details:
  call: sysfonts::font_add("wqy-microhei", out_file)
  error: freetype: unknown file format, error code 2
Execution halted

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
Error: .onLoad failed in loadNamespace() for 'showtext', details:
  call: sysfonts::font_add("wqy-microhei", out_file)
  error: freetype: unknown file format, error code 2
In addition: Warning message:
In utils::unzip(font_file, exdir = out_dir, overwrite = FALSE) :
  write error in extracting from zip file
Execution halted
Loading required package: optimizeR
Error: package or namespace load failed for ‘ao’:
 .onLoad failed in loadNamespace() for 'showtext', details:
  call: sysfonts::font_add("wqy-microhei", out_file)
  error: freetype: unknown file format, error code 2
In addition: Warning message:
In utils::unzip(font_file, exdir = out_dir, overwrite = FALSE) :
  write error in extracting from zip file
Execution halted

It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
Error: package or namespace load failed for ‘ao’:
 .onLoad failed in loadNamespace() for 'showtext', details:
  call: sysfonts::font_add("wqy-microhei", out_file)
  error: freetype: unknown file format, error code 2
Call sequence:
Execution halted
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
'LazyData' is specified without a 'data' directory
installed size is 33.2Mb
  sub-directories of 1Mb or more:
    libs  32.9Mb
Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs   3.0Mb
Namespaces in Imports field not imported from:
  ‘AER’ ‘ChainLadder’ ‘ISLR’ ‘ggplot2’
  All declared Imports should be used.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    documents     2.4Mb
    libs          5.5Mb
    screenshots   1.6Mb
'LazyData' is specified without a 'data' directory
installed size is 29.9Mb
  sub-directories of 1Mb or more:
    libs  29.6Mb
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    extdata   5.4Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    data   1.6Mb
    doc    1.8Mb
Package suggested but not available for checking: ‘arcgisbinding’
Namespaces in Imports field not imported from:
  ‘bannerCommenter’ ‘config’ ‘feather’ ‘here’ ‘knitr’ ‘log4r’ ‘ps’
  ‘rmarkdown’ ‘skimr’ ‘snakecase’ ‘testthat’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    libs  17.9Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘purrr’ ‘shinyBS’ ‘shinydashboard’ ‘shinyjs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Packages suggested but not available for checking:
  'oligo', 'oligoClasses', 'pdInfoBuilder', 'AffymetrixDataTestFiles'
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R             3.1Mb
    help          1.1Mb
    testScripts   1.1Mb
Packages unavailable to check Rd xrefs: ‘oligo’, ‘oligoClasses’
Packages suggested but not available for checking:
  'sfit', 'expectile', 'HaarSeg', 'mpcbs'
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
'LazyData' is specified without a 'data' directory
installed size is 67.9Mb
  sub-directories of 1Mb or more:
    R      5.1Mb
    libs  62.2Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Running ‘testthat.R’ [17s/21s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  `actual`:   "2022-06-26 22:41:55" "2021-08-09 21:49:06"
  `expected`: "2022-06-27 22:41:50" "2021-08-10 21:47:13"
  ── Failure ('test-06_calc_sun.R:95:3'): calc_ss_diff() ─────────────────────────
  all(dplyr::select(diff, starts_with("t2")) < 48 * 60) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 3 | WARN 0 | SKIP 6 | PASS 488 ]
  Deleting unused snapshots:
  • 08_selections/sim-selection-weights2.svg
  • 08_selections/sim-selection-weights3.svg
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    include   6.4Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   9.0Mb
Package which this enhances but not available for checking: ‘asreml’
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘asteRiskData’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   1.5Mb
GNU make is a SystemRequirements.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.0Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘abind’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
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'LazyData' is specified without a 'data' directory
installed size is 18.3Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Hmisc’
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Namespaces in Imports field not imported from:
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installed size is 23.7Mb
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Namespaces in Imports field not imported from:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘openssl’
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Namespaces in Imports field not imported from:
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Namespaces in Imports field not imported from:
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Namespace in Imports field not imported from: ‘R6’
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installed size is  7.4Mb
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Package suggested but not available for checking: ‘lixoftConnectors’
Note: found 64209 marked UTF-8 strings
installed size is  6.1Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘pcalg’
Package unavailable to check Rd xrefs: ‘pcalg’
installed size is 115.0Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 95.7Mb
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GNU make is a SystemRequirements.
installed size is 63.5Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
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'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
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installed size is  5.7Mb
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Package suggested but not available for checking: ‘fdpbandsdata’
installed size is  5.7Mb
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'LazyData' is specified without a 'data' directory
Note: found 148 marked UTF-8 strings
Package suggested but not available for checking: ‘ArrayExpress’
'LazyData' is specified without a 'data' directory
installed size is  9.4Mb
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installed size is  8.0Mb
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installed size is 13.6Mb
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Namespace in Imports field not imported from: ‘splines’
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘doMPI’
Package unavailable to check Rd xrefs: ‘Rmpi’
Namespace in Imports field not imported from: ‘vtable’
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installed size is 70.7Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
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installed size is 118.1Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
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installed size is  5.4Mb
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Namespaces in Imports field not imported from:
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'LazyData' is specified without a 'data' directory
installed size is 24.4Mb
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Package suggested but not available for checking: ‘INLA’
installed size is 11.2Mb
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installed size is 70.3Mb
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Namespaces in Imports field not imported from:
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GNU make is a SystemRequirements.
installed size is 96.7Mb
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Namespaces in Imports field not imported from:
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GNU make is a SystemRequirements.
installed size is 114.0Mb
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GNU make is a SystemRequirements.
installed size is 45.9Mb
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GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘plyr’
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'LazyData' is specified without a 'data' directory
installed size is 58.8Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
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installed size is  8.0Mb
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installed size is  8.7Mb
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GNU make is a SystemRequirements.
installed size is 10.4Mb
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installed size is 13.5Mb
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Namespace in Imports field not imported from: ‘FastGP’
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installed size is 25.9Mb
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installed size is  5.3Mb
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'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
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installed size is 11.0Mb
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Namespaces in Imports field not imported from:
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installed size is 12.9Mb
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installed size is  8.1Mb
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Note: found 1924 marked UTF-8 strings
installed size is 86.3Mb
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Namespaces in Imports field not imported from:
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GNU make is a SystemRequirements.
installed size is 18.2Mb
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installed size is  5.5Mb
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installed size is  5.8Mb
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Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
installed size is  7.0Mb
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installed size is 10.8Mb
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GNU make is a SystemRequirements.
installed size is 32.0Mb
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GNU make is a SystemRequirements.
installed size is  5.4Mb
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Namespaces in Imports field not imported from:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
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Error(s) in re-building vignettes:
--- re-building ‘article.Rnw’ using Sweave
Setting levels: control = No, case = Yes
Loading required package: glmnet
Loading required package: Matrix
Loaded glmnet 4.1-7
Setting levels: control = No, case = Yes
Setting levels: control = No, case = Yes
Loading required package: Biostrings
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated,
    append, as.data.frame, basename, cbind, colnames, dirname,
    do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    expand, unname

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: XVector
Loading required package: GenomeInfoDb

Attaching package: 'Biostrings'

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

    strsplit

Error: processing vignette 'article.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'article.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 657 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'article.Rnw'

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

Error: Vignette re-building failed.
Execution halted
installed size is 34.1Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘mixAK’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.8Mb
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GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘BRugs’
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘flowCore’
installed size is 96.7Mb
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GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
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installed size is  7.8Mb
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'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [30s/36s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-formattedCombiner.R:61:1'): (code run outside of `test_that()`) ──
  Error in `file(.)`: invalid 'description' argument
  Backtrace:
      ▆
   1. ├─BeeBDC::formattedCombiner(...) at test-formattedCombiner.R:61:1
   2. │ └─... %>% xml2::read_xml()
   3. ├─xml2::read_xml(.)
   4. └─base::file(.)
  
  [ FAIL 1 | WARN 3 | SKIP 0 | PASS 238 ]
  Error: Test failures
  Execution halted
  Warning message:
  Connection is garbage-collected, use dbDisconnect() to avoid this.
installed size is 47.8Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 14.4Mb
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'LazyData' is specified without a 'data' directory
installed size is 47.4Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 36.5Mb
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GNU make is a SystemRequirements.
installed size is 52.3Mb
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GNU make is a SystemRequirements.
installed size is 25.4Mb
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Namespace in Imports field not imported from: ‘BiDAG’
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installed size is 60.6Mb
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is 13.1Mb
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installed size is 10.3Mb
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GNU make is a SystemRequirements.
installed size is 163.0Mb
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installed size is  5.4Mb
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'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
Namespace in Imports field not imported from: ‘nycflights13’
  All declared Imports should be used.
installed size is  9.6Mb
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Namespace in Imports field not imported from: ‘httr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘INLA’
installed size is  5.6Mb
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installed size is  6.2Mb
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Package required but not available: ‘Rmpi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.3Mb
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installed size is  6.3Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rrelaxiv’
installed size is  7.2Mb
  sub-directories of 1Mb or more:
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installed size is  9.2Mb
  sub-directories of 1Mb or more:
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installed size is 27.7Mb
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installed size is  9.3Mb
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Namespace in Imports field not imported from: ‘rmio’
  All declared Imports should be used.
installed size is 12.0Mb
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Namespace in Imports field not imported from: ‘rmio’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
installed size is  5.6Mb
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installed size is 19.7Mb
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Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Note: found 660 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘gtools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
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'LazyData' is specified without a 'data' directory
installed size is 92.3Mb
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GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘msa’
installed size is  6.3Mb
  sub-directories of 1Mb or more:
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installed size is  6.0Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘asreml’
installed size is  5.5Mb
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installed size is  6.1Mb
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installed size is  8.2Mb
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Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
installed size is  6.1Mb
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Note: found 46 marked UTF-8 strings
Package listed in more than one of Depends, Imports, Suggests, Enhances:
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A package should be listed in only one of these fields.
Packages in Depends field not imported from:
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  These packages need to be imported from (in the NAMESPACE file)
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is  6.5Mb
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installed size is 38.6Mb
  sub-directories of 1Mb or more:
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is  6.4Mb
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Namespaces in Imports field not imported from:
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Package suggested but not available for checking: ‘cmdstanr’
installed size is 159.0Mb
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GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is  8.5Mb
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'LazyData' is specified without a 'data' directory
installed size is 33.8Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
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installed size is 14.1Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 7 marked UTF-8 strings
installed size is 167.8Mb
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GNU make is a SystemRequirements.
installed size is 95.2Mb
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is 50.4Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is 90.8Mb
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GNU make is a SystemRequirements.
installed size is  6.7Mb
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Namespace in Imports field not imported from: ‘dplyr’
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Namespaces in Imports field not imported from:
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installed size is 16.2Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
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Namespaces in Imports field not imported from:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
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Package suggested but not available for checking: ‘sangerseqR’
installed size is 13.1Mb
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installed size is 396.6Mb
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GNU make is a SystemRequirements.
installed size is 93.4Mb
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Namespace in Imports field not imported from: ‘sna’
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
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GNU make is a SystemRequirements.
Packages suggested but not available for checking: 'cplexAPI', 'bestsubset'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
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installed size is 52.5Mb
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GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
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'LazyData' is specified without a 'data' directory
installed size is  8.0Mb
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'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 38.9Mb
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GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘kableExtra’
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'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
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Package suggested but not available for checking: ‘cmdstanr’
installed size is  8.9Mb
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Package suggested but not available for checking: ‘glmmADMB’
installed size is  5.4Mb
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'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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installed size is 11.7Mb
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GNU make is a SystemRequirements.
installed size is 31.8Mb
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 110.9Mb
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installed size is 12.1Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
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installed size is  6.2Mb
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'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.3Mb
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installed size is 21.5Mb
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'LazyData' is specified without a 'data' directory
installed size is 116.7Mb
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Malformed Description field: should contain one or more complete sentences.
Package suggested but not available for checking: ‘doMPI’
installed size is 19.3Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 129.6Mb
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installed size is 43.2Mb
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Namespaces in Imports field not imported from:
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘markdown’
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installed size is 62.5Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ReGenesees’
'LazyData' is specified without a 'data' directory
installed size is  9.8Mb
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'LazyData' is specified without a 'data' directory
Package required but not available: ‘org.Dr.eg.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
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Note: found 287 marked UTF-8 strings
Package required but not available: ‘bluster’

Package suggested but not available for checking: ‘scran’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Note: found 59 marked UTF-8 strings
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
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installed size is 10.6Mb
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Note: found 1 marked UTF-8 string
installed size is  8.1Mb
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Namespaces in Imports field not imported from:
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'LazyData' is specified without a 'data' directory
installed size is 10.9Mb
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installed size is 37.8Mb
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GNU make is a SystemRequirements.
Found the following apparent S3 methods exported but not registered:
  simulate.carms
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
S3 methods shown with full name in documentation object 'simulate.carms':
  ‘simulate.carms’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rnaturalearthhires’
Namespace in Imports field not imported from: ‘R.utils’
  All declared Imports should be used.
installed size is 12.2Mb
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GNU make is a SystemRequirements.
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Namespaces in Imports field not imported from:
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'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 21.2Mb
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Running ‘testthat.R’ [234s/265s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  `expected`: 0.9530
  ── Failure ('test-global_validation.R:20:3'): global_validation works with caret regression ──
  global_validation(model) (`actual`) not equal to c(RMSE = 0.330787, Rsquared = 0.8400544, MAE = 0.2621827) (`expected`).
  
    `actual`: 0.332 0.838 0.258
  `expected`: 0.331 0.840 0.262
  ── Failure ('test-global_validation.R:48:3'): global_validation works with CreateSpacetimeFolds ──
  global_validation(model)[1:2] (`actual`) not equal to c(Accuracy = 0.96, Kappa = 0.94) (`expected`).
  
    `actual`: 0.953 0.930
  `expected`: 0.960 0.940
  
  [ FAIL 6 | WARN 0 | SKIP 0 | PASS 128 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
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installed size is 20.2Mb
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'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
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Namespaces in Imports field not imported from:
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installed size is  7.6Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 32 marked UTF-8 strings
installed size is  6.5Mb
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installed size is 53.5Mb
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GNU make is a SystemRequirements.
installed size is  7.4Mb
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installed size is  6.5Mb
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'LazyData' is specified without a 'data' directory
installed size is 163.3Mb
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GNU make is a SystemRequirements.
installed size is 17.2Mb
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Namespace in Imports field not imported from: ‘GeneNet’
  All declared Imports should be used.
installed size is  5.8Mb
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'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘fields’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 22.3Mb
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Packages which this enhances but not available for checking:
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installed size is  6.2Mb
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installed size is  5.9Mb
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'LazyData' is specified without a 'data' directory
installed size is 15.1Mb
  sub-directories of 1Mb or more:
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installed size is 11.2Mb
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Unexported objects imported by ':::' calls:
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  See the note in ?`:::` about the use of this operator.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lmtest’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 37.9Mb
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Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
installed size is  6.4Mb
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is  5.0Mb
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'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
Package suggested but not available for checking: ‘pbdMPI’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dbplyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gamlss.dist’
  All declared Imports should be used.
Note: found 32 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Package unavailable to check Rd xrefs: ‘cmdstanr’
installed size is  5.0Mb
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installed size is  5.5Mb
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installed size is 18.0Mb
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘entab’
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is  8.0Mb
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Namespace in Imports field not imported from: ‘R6’
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
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'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘magrittr’
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Packages required but not available:
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Note: found 28982 marked UTF-8 strings
Package suggested but not available for checking: ‘userfriendlyscience’
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
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Namespaces in Imports field not imported from:
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'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
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installed size is  5.2Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘RColorBrewer’
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Namespace in Imports field not imported from: ‘networkD3’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 14.6Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
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installed size is 10.4Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
installed size is  9.3Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
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installed size is 48.6Mb
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installed size is  5.5Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
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installed size is 17.1Mb
  sub-directories of 1Mb or more:
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installed size is 32.2Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
installed size is  6.9Mb
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'LazyData' is specified without a 'data' directory
installed size is 16.5Mb
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'LazyData' is specified without a 'data' directory
installed size is  9.3Mb
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Namespaces in Imports field not imported from:
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Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
Note: found 5626 marked UTF-8 strings
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 15.9Mb
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installed size is  6.1Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 34.9Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Package required but not available: ‘GenomicInteractions’

Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg19’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.2Mb
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Package suggested but not available for checking: ‘disttree’
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘rkward’
Package which this enhances but not available for checking: ‘rkward’
Package suggested but not available for checking: ‘userfriendlyscience’
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
Note: found 65 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
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Namespaces in Imports field not imported from:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 14.3Mb
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Note: found 4186 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
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Namespaces in Imports field not imported from:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 742 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘grid’ ‘gridExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Running examples in ‘colorspace-Ex.R’ failed
The error most likely occurred in:

> ### Name: scale_colour_binned_diverging
> ### Title: HCL-Based Binned Diverging Color Scales for ggplot2
> ### Aliases: scale_colour_binned_diverging scale_color_binned_diverging
> ###   scale_fill_binned_diverging
> 
> ### ** Examples
> 
> # adapted from stackoverflow: https://stackoverflow.com/a/20127706/4975218
> 
> library("ggplot2")
Error: package or namespace load failed for ‘ggplot2’:
 .onAttach failed in attachNamespace() for 'ggplot2', details:
  call: loadNamespace(x)
  error: there is no package called ‘withr’
Execution halted
installed size is  5.3Mb
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    extdata   2.1Mb
installed size is 52.5Mb
  sub-directories of 1Mb or more:
    libs  51.7Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
Namespaces in Imports field not imported from:
  ‘chi’ ‘dplyr’ ‘spatstat.utils’ ‘utils’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  15.2Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    java   6.7Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Namespaces in Imports field not imported from:
  ‘GGally’ ‘RColorBrewer’ ‘abind’ ‘diagram’ ‘ggplot2’ ‘grid’ ‘gtable’
  ‘igraph’ ‘magrittr’ ‘plyr’ ‘purrr’ ‘reshape2’ ‘scales’ ‘useful’
  All declared Imports should be used.
Package suggested but not available for checking: ‘CAM’
installed size is 30.5Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs  28.4Mb
Namespaces in Imports field not imported from:
  ‘PearsonDS’ ‘VGAM’ ‘actuar’ ‘fExtremes’ ‘rmutil’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
'LazyData' is specified without a 'data' directory
Package required but not available: ‘R4RNA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
Note: found 92 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘kernlab’ ‘purrr’ ‘survminer’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
Namespaces in Imports field not imported from:
  ‘base’ ‘lwgeom’ ‘s2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘Hmisc’ ‘dplyr’ ‘foreign’ ‘lavaan’ ‘openxlsx’ ‘purrr’ ‘semTools’
  ‘shinyWidgets’ ‘stringr’ ‘summarytools’ ‘waiter’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'conosPanel', 'p2data'
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    libs  19.9Mb
Namespaces in Imports field not imported from:
  ‘scales’ ‘sna’
  All declared Imports should be used.
Note: found 244 marked UTF-8 strings
installed size is 68.5Mb
  sub-directories of 1Mb or more:
    libs  67.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc             2.2Mb
    vignette_data   2.6Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   2.1Mb
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    help   2.6Mb
    libs   3.3Mb
Packages required and available but unsuitable versions:
  'stats', 'grDevices'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘cec2005benchmark’
'LazyData' is specified without a 'data' directory
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R     2.4Mb
    doc   3.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs          2.8Mb
    sample_data   2.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘ggplot2’ ‘re2’ ‘rmarkdown’ ‘shinyWidgets’
  ‘shinydashboard’ ‘shinyjs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   3.8Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ProData’
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    extdata  17.7Mb
fishp: no visible binding for global variable ‘markname’
fishp: no visible binding for global variable ‘sum_chisq’
fishp: no visible binding for global variable ‘sum_z’
pvalues_to_zscores: no visible binding for global variable ‘markname’
tetracorr: no visible binding for global variable ‘PLCORR’
Undefined global functions or variables:
  PLCORR markname sum_chisq sum_z
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc   6.7Mb
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
Namespace in Imports field not imported from: ‘jpeg’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   5.3Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    extdata   2.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
Note: found 1934235 marked UTF-8 strings
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘httr’ ‘stringr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘mapview’ ‘plotly’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘gsl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘misc3d’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘mediation’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    2.9Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘grDevices’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘cplm.Rnw’ using Sweave
Loading required package: coda
Loading required package: Matrix
Loading required package: splines
Error: processing vignette 'cplm.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'cplm.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 600 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘cplm.Rnw’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
GNU make is a SystemRequirements.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   2.9Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    2.2Mb
    libs   5.5Mb
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
Note: found 11 marked Latin-1 strings
  Note: found 57 marked UTF-8 strings
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is 41.5Mb
  sub-directories of 1Mb or more:
    libs  41.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘BSgenome.Scerevisiae.UCSC.sacCer3’
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   6.4Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘dplyr’ ‘r6extended’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 500 marked UTF-8 strings
installed size is 28.2Mb
  sub-directories of 1Mb or more:
    libs  26.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
Package suggested but not available for checking: ‘INLA’
Namespaces in Imports field not imported from:
  ‘DT’ ‘dplyr’ ‘geosphere’ ‘mapdata’ ‘maps’ ‘marmap’ ‘shinydashboard’
  ‘shinyjs’ ‘stringr’ ‘swfscDAS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘extrafont’ ‘future’
  All declared Imports should be used.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    doc    1.6Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   7.9Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   8.0Mb
Namespaces in Imports field not imported from:
  ‘epitools’ ‘rpivotTable’ ‘shinyMatrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1350 marked UTF-8 strings
installed size is 177.3Mb
  sub-directories of 1Mb or more:
    R       2.1Mb
    data    2.1Mb
    libs  171.8Mb
GNU make is a SystemRequirements.
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
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
'LazyData' is specified without a 'data' directory
Package required and available but unsuitable version: ‘IRanges’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘pbdMPI’
Namespace in Imports field not imported from: ‘pspearman’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘curl/libs/curl.so’:
  Found non-API call to R: ‘R_new_custom_connection’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘RGtk2’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Packages which this enhances but not available for checking:
  'Rcplex', 'gurobi', 'rcbc'
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    doc    1.2Mb
    libs   4.6Mb
installed size is 22.7Mb
  sub-directories of 1Mb or more:
    libs  21.8Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    docs          1.0Mb
    extdata       1.3Mb
    htmlwidgets   1.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    1.1Mb
    libs   3.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Namespace in Imports field not imported from: ‘titanic’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 109157 marked UTF-8 strings
Note: found 2020 marked UTF-8 strings
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
installed size is 29.3Mb
  sub-directories of 1Mb or more:
    libs  27.3Mb
Warning: declared S3 method 'transform.bal_oversampling' not found
Warning: declared S3 method 'transform.bal_subsampling' not found
Warning: declared S3 method 'transform.fs' not found
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Note: found 5 marked UTF-8 strings
str:
  function(object, ...)
str.language:
  function(expr, name, indent)

See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.

Found the following apparent S3 methods exported but not registered:
  str.language
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    help   2.2Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    java   7.5Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   3.9Mb
GNU make is a SystemRequirements.
Packages required and available but unsuitable versions: 'methods', 'utils'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘msa’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘knitr’ ‘tidyverse’ ‘vctrs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘softImpute’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   6.4Mb
'LazyData' is specified without a 'data' directory
Package required but not available: ‘RedeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Note: found 122 marked UTF-8 strings
Package suggested but not available for checking: ‘BRugs’
Package suggested but not available for checking: ‘INLA’
Note: found 2 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 52.1Mb
  sub-directories of 1Mb or more:
    libs  51.7Mb
Note: found 38 marked UTF-8 strings
GNU make is a SystemRequirements.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs   5.6Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
'LazyData' is specified without a 'data' directory
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    libs  24.2Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
Package required and available but unsuitable version: ‘ggtree’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘BSgenome.Hsapiens.UCSC.hg19’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘knitr’ ‘shinyBS’ ‘shinyMatrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.1Mb
    help   1.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 38.0Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs  35.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc       4.8Mb
    extdata   2.1Mb
Package suggested but not available for checking: ‘Rdonlp2’
Package suggested but not available for checking: ‘Rdonlp2’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 5764 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RDCOMClient’
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    1.8Mb
    help   1.6Mb
    libs   3.2Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘OSAT’
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex'
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
    libs      2.2Mb
'LazyData' is specified without a 'data' directory
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  12.0Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data          1.8Mb
    htmlwidgets   3.7Mb
GNU make is a SystemRequirements.
installed size is 19.6Mb
  sub-directories of 1Mb or more:
    libs  18.8Mb
Namespace in Imports field not imported from: ‘RColorBrewer’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   8.0Mb
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'signatureSearch', 'signatureSearchData'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   4.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  14.4Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
'LazyData' is specified without a 'data' directory
Note: found 8014 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘R6’ ‘dplyr’ ‘purrr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    doc  10.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
'LazyData' is specified without a 'data' directory
Packages required but not available: 'zinbwave', 'scran'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rrelaxiv’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is 32.4Mb
  sub-directories of 1Mb or more:
    libs  31.8Mb
installed size is 69.8Mb
  sub-directories of 1Mb or more:
    libs  69.0Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘readr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   4.2Mb
Package which this enhances but not available for checking: ‘INLA’
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [4s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  realized_duration(...) not equal to c(...).
  1/4 mismatches
  [1] 29 - 28 == 1
  ── Failure ('test-realized_duration.R:158:2'): realized_duration works (realized_only = TRUE) ──
  realized_duration(...) not equal to c(...).
  1/4 mismatches
  [2] 29 - 28 == 1
  ── Failure ('test-realized_duration.R:161:2'): realized_duration works (realized_only = TRUE) ──
  realized_duration(...) not equal to c(...).
  1/4 mismatches
  [1] 29 - 28 == 1
  
  [ FAIL 36 | WARN 0 | SKIP 0 | PASS 331 ]
  Error: Test failures
  Execution halted
Note: found 12 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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installed size is  7.6Mb
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Package suggested but not available for checking: ‘BOLTSSIRR’
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Namespaces in Imports field not imported from:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.2Mb
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Namespace in Imports field not imported from: ‘MASS’
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installed size is 34.2Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
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installed size is  7.3Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 19.8Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
Package which this enhances but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Rmpi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
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Note: found 100 marked UTF-8 strings
Namespace in Imports field not imported from: ‘gridExtra’
  All declared Imports should be used.
Package suggested but not available for checking: ‘doMPI’
Package unavailable to check Rd xrefs: ‘doMPI’
Package suggested but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
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installed size is  5.2Mb
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
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Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 13.2Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘TxDb.Hsapiens.UCSC.hg38.knownGene’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is  9.6Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/DRviaSPCN.Rcheck/00install.out’ for details.
installed size is  5.2Mb
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is 84.3Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘dsBaseClient’
Package required and available but unsuitable version: ‘stats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
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installed size is 12.3Mb
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installed size is  9.0Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 371.0Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
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Package suggested but not available for checking: ‘cmdstanr’
installed size is 14.0Mb
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Package unavailable to check Rd xrefs: ‘cmdstanr’
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.0Mb
  sub-directories of 1Mb or more:
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    libs   2.9Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   1.2Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘hms’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
File ‘eaf/libs/eaf.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
    Objects: ‘eaf/io.o’, ‘mo-tools/hv.o’
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
    Object: ‘eaf/io.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
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    shiny_app   1.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
installed size is 13.7Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘diffcoexp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘gurobi’
Namespace in Imports field not imported from: ‘RSQLite’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘qcr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 13.6Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘pander’
  All declared Imports should be used.
installed size is 127.1Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.4Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magrittr’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘opGMMassessment’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘PCovR’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 27.2Mb
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Note: found 24 marked UTF-8 strings
Package suggested but not available for checking: ‘eggCountsExtra’
installed size is 94.4Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(EGRETci)
  > test_check("EGRETci")
  [ FAIL 1 | WARN 0 | SKIP 10 | PASS 16 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (10)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('tests_boot_tests.R:112:3'): paVector ──────────────────────────────
  `paIndexWinter` not equal to 11:13.
  Lengths differ: 4 is not 3
  
  [ FAIL 1 | WARN 0 | SKIP 10 | PASS 16 ]
  Error: Test failures
  Execution halted
installed size is 11.5Mb
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installed size is 142.4Mb
  sub-directories of 1Mb or more:
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installed size is 43.1Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is 25.6Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘datasets’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 61.7Mb
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GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is  9.4Mb
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'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
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installed size is  7.0Mb
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Note: found 16919 marked UTF-8 strings
Note: found 23639 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is  7.3Mb
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Package suggested but not available for checking: ‘Rmpi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.1Mb
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'LazyData' is specified without a 'data' directory
checkRd: (5) ePCR.Rd:0-17: Must have a \description
installed size is  5.6Mb
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Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tinytest’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
installed size is  6.1Mb
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Package suggested but not available for checking: ‘epidict’
installed size is 107.6Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘taskscheduleR’
installed size is 13.1Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gcspikelite’
installed size is  5.6Mb
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installed size is  7.4Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 14.1Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 39.9Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘metadat’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘EnvStats’
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'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
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installed size is  7.5Mb
  sub-directories of 1Mb or more:
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installed size is  5.9Mb
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'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘parallel’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘ExactData’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘INLA’
installed size is 14.1Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
installed size is  8.8Mb
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'LazyData' is specified without a 'data' directory
installed size is 95.3Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.0Mb
  sub-directories of 1Mb or more:
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Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘exuberdata’
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘BiocStyle’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Warning: declared S3 method 'forecast.GLARMA' not found
Warning: declared S3 method 'forecast.INGARCH' not found
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
installed size is  7.6Mb
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'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
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Error(s) in re-building vignettes:
--- re-building ‘jss.Rmd’ using rmarkdown
This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode

kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+57/600 --dpi 657 bbm10
mkdir: ././opt/tex/texmf-var/fonts/pk/ljfour/public: Permission denied
mktexpk: /opt/tex/texmf-dist/web2c/mktexdir /opt/tex/texmf-var/fonts/pk/ljfour/public/bbm failed.
kpathsea: Appending font creation commands to missfont.log.
This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode

kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+57/600 --dpi 657 bbm10
mkdir: ././opt/tex/texmf-var/fonts/pk/ljfour/public: Permission denied
mktexpk: /opt/tex/texmf-dist/web2c/mktexdir /opt/tex/texmf-var/fonts/pk/ljfour/public/bbm failed.
kpathsea: Appending font creation commands to missfont.log.
This is pdfTeX, Version 3.141592653-2.6-1.40.24 (TeX Live 2022) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode

kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+57/600 --dpi 657 bbm10
mkdir: ././opt/tex/texmf-var/fonts/pk/ljfour/public: Permission denied
mktexpk: /opt/tex/texmf-dist/web2c/mktexdir /opt/tex/texmf-var/fonts/pk/ljfour/public/bbm failed.
kpathsea: Appending font creation commands to missfont.log.
Error: processing vignette 'jss.Rmd' failed with diagnostics:
LaTeX failed to compile /Volumes/Builds/packages/big-sur-arm64/results/4.2/fairadapt.Rcheck/vign_test/fairadapt/vignettes/jss.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips.
--- failed re-building ‘jss.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is  6.4Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.4Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  5.1Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 25.3Mb
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installed size is  5.8Mb
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installed size is 10.3Mb
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Namespace in Imports field not imported from: ‘RobustGaSP’
  All declared Imports should be used.
installed size is  7.2Mb
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installed size is  8.3Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
installed size is 47.4Mb
  sub-directories of 1Mb or more:
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installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is 49.2Mb
  sub-directories of 1Mb or more:
    libs  48.9Mb
Package suggested but not available for checking: ‘coxKM’
installed size is  8.5Mb
  sub-directories of 1Mb or more:
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    libs   2.6Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  14.4Mb
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
installed size is 16.1Mb
  sub-directories of 1Mb or more:
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.run: no visible binding for global variable ‘init’
.run: no visible global function definition for ‘init’
.run: no visible binding for global variable ‘run’
Undefined global functions or variables:
  init run
Note: information on .o files is not available
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.7Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
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    libs   5.5Mb
Package suggested but not available for checking: ‘NNLM’
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
    libs   4.8Mb
GNU make is a SystemRequirements.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   2.3Mb
'LazyData' is specified without a 'data' directory
installed size is 33.4Mb
  sub-directories of 1Mb or more:
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs  10.3Mb
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    3.9Mb
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
'LazyData' is specified without a 'data' directory
installed size is 14.2Mb
  sub-directories of 1Mb or more:
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Unexported object imported by a ':::' call: ‘fdapace:::interp2lin’
  See the note in ?`:::` about the use of this operator.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
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installed size is 40.2Mb
  sub-directories of 1Mb or more:
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installed size is 11.9Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is 17.1Mb
  sub-directories of 1Mb or more:
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installed size is 24.8Mb
  sub-directories of 1Mb or more:
    libs  24.4Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.4Mb
Note: found 76 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘data.table’ ‘ggplot2’ ‘randomcoloR’ ‘sqldf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘e1071’ ‘lattice’ ‘randomForest’ ‘tibble’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘panelView’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘rvest’ ‘stringi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data      2.0Mb
    extdata   2.8Mb
    libs      1.2Mb
Namespace in Imports field not imported from: ‘numDeriv’
  All declared Imports should be used.
Package suggested but not available for checking: ‘MicrobeDS’
installed size is 39.8Mb
  sub-directories of 1Mb or more:
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installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
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    help   1.1Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    R         5.7Mb
    doc       2.1Mb
    extdata   2.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘rclipboard’ ‘shinyBS’ ‘shinyWidgets’ ‘shinyjs’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
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    libs   7.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
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    extdata   2.8Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RcppProgress’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is 34.2Mb
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Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’ ‘utils’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    extdata   3.8Mb
'LazyData' is specified without a 'data' directory
installed size is 30.2Mb
  sub-directories of 1Mb or more:
    lib   10.3Mb
    libs  19.5Mb
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘fitbitScraper-examples.Rmd’ using rmarkdown
Quitting from lines 22-24 (fitbitScraper-examples.Rmd) 
Error: processing vignette 'fitbitScraper-examples.Rmd' failed with diagnostics:
login failed
--- failed re-building ‘fitbitScraper-examples.Rmd’

SUMMARY: processing the following file failed:
  ‘fitbitScraper-examples.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   4.0Mb
Package suggested but not available for checking: ‘gridlayout’
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rstudioapi’
  All declared Imports should be used.
Package suggested but not available for checking: ‘fivethirtyeightdata’
Package unavailable to check Rd xrefs: ‘fivethirtyeightdata’
Found the following apparent S3 methods exported but not registered:
  plot.fpp
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    3.6Mb
    libs   5.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
  sub-directories of 1Mb or more:
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    help   2.3Mb
    libs   3.3Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘RCurl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 300.5Mb
  sub-directories of 1Mb or more:
    libs  299.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Note: found 710 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 10.6Mb
  sub-directories of 1Mb or more:
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installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    R   7.1Mb
Malformed Description field: should contain one or more complete sentences.
installed size is 25.8Mb
  sub-directories of 1Mb or more:
    libs  25.5Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    fonts   6.6Mb
Malformed Description field: should contain one or more complete sentences.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    fonts   6.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘minet’
Namespace in Imports field not imported from: ‘grid’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dtplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘decomposedPSF’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘blockCV’ ‘patchwork’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘pkgKitten’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘tibble’ ‘viridis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   6.9Mb
Note: found 31 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘LaplacesDemon’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
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    libs   6.2Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R   6.6Mb
Note: found 50 marked UTF-8 strings
Packages suggested but not available for checking: 'dggrids', 'INLA'
installed size is 105.3Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
    doc    1.8Mb
    libs  97.5Mb
installed size is 35.9Mb
  sub-directories of 1Mb or more:
    libs  35.4Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'foba', 'rrlda'
Package suggested but not available for checking: ‘RTCGA.rnaseq’
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
Namespaces in Imports field not imported from:
  ‘class’ ‘mlbench’ ‘neuralnet’ ‘rpart’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    libs  14.2Mb
Namespace in Imports field not imported from: ‘qpdf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 39 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘foreach’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Note: found 120 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘FunWithNumbers-Ex.R’ failed
The error most likely occurred in:

> ### Name: aliquot
> ### Title: Generate the Aliquot Sequence.
> ### Aliases: aliquot
> 
> ### ** Examples
> 
> aliquot(20)
Error in if (aliseq[j] %in% aliseq[1:(j - 1)]) { : 
  the condition has length > 1
Calls: aliquot
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘WGCNA’
Package suggested but not available for checking: ‘IRanges’
Package unavailable to check Rd xrefs: ‘IRanges’
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    help   4.2Mb
installed size is 37.7Mb
  sub-directories of 1Mb or more:
    libs  37.5Mb
installed size is 25.8Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs  22.2Mb
Namespaces in Imports field not imported from:
  ‘gargle’ ‘getProxy’ ‘rappsflyer’ ‘rfacebookstat’ ‘rgoogleads’
  ‘rmytarget’ ‘rvkstat’ ‘ryandexdirect’ ‘rym’ ‘tidyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Package which this enhances but not available for checking: ‘doMPI’
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc   7.9Mb
installed size is 36.1Mb
  sub-directories of 1Mb or more:
    doc   31.8Mb
    libs   3.8Mb
'LazyData' is specified without a 'data' directory
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs  10.1Mb
installed size is 84.8Mb
  sub-directories of 1Mb or more:
    libs  84.3Mb
GNU make is a SystemRequirements.
installed size is 59.4Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     55.8Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   6.6Mb
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  15.7Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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.
Package suggested but not available for checking: ‘gputools’
Error(s) in re-building vignettes:
  ...
--- re-building ‘gcbd.Rnw’ using Sweave
Warning in packageDescription("gputools") :
  no package 'gputools' was found
Error: processing vignette 'gcbd.Rnw' failed with diagnostics:
at gcbd.Rnw:860, subscript out of bounds
--- failed re-building ‘gcbd.Rnw’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 273.6Mb
  sub-directories of 1Mb or more:
    L8NY18    2.2Mb
    libs    270.1Mb
installed size is 252.8Mb
  sub-directories of 1Mb or more:
    libs  250.4Mb
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
Namespace in Imports field not imported from: ‘badger’
  All declared Imports should be used.
Package suggested but not available for checking: ‘gdxrrw’
'LazyData' is specified without a 'data' directory
Running examples in ‘GEC-Ex.R’ failed
The error most likely occurred in:

> ### Name: eep_optim
> ### Title: The Wrapper Function that Returns the Final Estimates from
> ###   Maximum Likelihood Estimation for EEP.
> ### Aliases: eep_optim
> 
> ### ** Examples
> 
> eep_optim(seq(1:100))
Error in stats::optim(init, lower = lower_bound, eep_nll, method = "L-BFGS-B",  : 
  L-BFGS-B needs finite values of 'fn'
Calls: eep_optim -> raw_est_eep -> <Anonymous>
Execution halted
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    libs  17.5Mb
Namespace in Imports field not imported from: ‘rootSolve’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   3.4Mb
    libs      1.4Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘pracma’ ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘genderdata’
Namespaces in Imports field not imported from:
  ‘BiocManager’ ‘R.utils’ ‘markdown’
  All declared Imports should be used.
Package suggested but not available for checking: ‘rrvgo’
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   9.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘GGEBiplots’ ‘calibrate’ ‘graphics’ ‘matrixStats’ ‘prettydoc’
  ‘reshape2’
  All declared Imports should be used.
Package required but not available: ‘biocViews’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   4.3Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 31.2Mb
  sub-directories of 1Mb or more:
    libs  30.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘geoAr_geofacet.Rmd’ using rmarkdown
File figure/tucmap-1.png not found in resource path
Error: processing vignette 'geoAr_geofacet.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building ‘geoAr_geofacet.Rmd’

--- re-building ‘geoAr_leaflet.Rmd’ using rmarkdown
File figure/map-1.png not found in resource path
Error: processing vignette 'geoAr_leaflet.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building ‘geoAr_leaflet.Rmd’

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

SUMMARY: processing the following files failed:
  ‘geoAr_geofacet.Rmd’ ‘geoAr_leaflet.Rmd’

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
    libs      4.0Mb
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc       2.1Mb
    extdata   3.5Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   4.8Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    help   1.3Mb
    libs   4.5Mb
Package suggested but not available for checking: ‘geomarocdata’
'LazyData' is specified without a 'data' directory
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    R        10.0Mb
    extdata   2.5Mb
    help      3.4Mb
Namespace in Imports field not imported from: ‘velociraptr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dbplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 102.4Mb
  sub-directories of 1Mb or more:
    libs  100.5Mb
GNU make is a SystemRequirements.
Package which this enhances but not available for checking: ‘INLA’
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is 34.1Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> ...s ,C_k)^\top = \mathbf {0}\,\,\text 
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l.238 ...H} (B_1,\ldots,B_k)^\top = \mathbf{0},}{}
                                                  
! Undefined control sequence.
<argument> ...\mathbf {C} = \mathbf {0}\,\, \text 
                                                  {or}\,\,\mathcal H_{0,\ell...
l.249 ...{B} = \mathbf{0}, \,\,\ell=1,\ldots,q,}{}
                                                  
! Undefined control sequence.
<argument> h_{\ell }^{\top }\pmb 
                                 {C}
l.251 ...s \eqn{\mathbf{h_{\ell}^{\top}\pmb{C}}}{}
                                                   and
! Undefined control sequence.
<argument> h_{\ell }^{\top }\pmb 
                                 {B}
l.252 \eqn{\mathbf{h_{\ell}^{\top}\pmb{B}}}{}
                                             , respectively, are calculated.
! Undefined control sequence.
<argument> h_{\ell }^{\top }\pmb 
                                 {C}
l.265 ...r \eqn{\mathbf{h_{\ell}^{\top}\pmb{C}}}{}
                                                   and
! Undefined control sequence.
<argument> h_{\ell }^{\top }\pmb 
                                 {B}
l.266 for \eqn{\mathbf{h_{\ell}^{\top}\pmb{B}}}{}
                                                 , the test statistics and c...
Package suggested but not available for checking: ‘RGtk2’
Namespaces in Imports field not imported from:
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installed size is 35.0Mb
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'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggmsa’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespace in Imports field not imported from: ‘plotly’
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.3Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.6Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 19.2Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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Namespace in Imports field not imported from: ‘utils’
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Namespaces in Imports field not imported from:
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Namespaces in Imports field not imported from:
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Namespaces in Imports field not imported from:
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Namespaces in Imports field not imported from:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘survival’
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'LazyData' is specified without a 'data' directory
Packages required but not available: 'lefser', 'Maaslin2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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Package suggested but not available for checking: ‘lixoftConnectors’
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Namespaces in Imports field not imported from:
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Namespace in Imports field not imported from: ‘dplyr’
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'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
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Namespaces in Imports field not imported from:
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Namespaces in Imports field not imported from:
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Namespace in Imports field not imported from: ‘tidyr’
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'LazyData' is specified without a 'data' directory
installed size is 11.0Mb
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Namespace in Imports field not imported from: ‘ggplot2’
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Namespace in Imports field not imported from: ‘class’
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Namespace in Imports field not imported from: ‘methods’
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installed size is  7.5Mb
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GNU make is a SystemRequirements.
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installed size is  8.8Mb
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'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
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installed size is  5.6Mb
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'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
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Namespaces in Imports field not imported from:
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Namespace in Imports field not imported from: ‘mockery’
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Namespaces in Imports field not imported from:
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Packages suggested but not available for checking:
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installed size is  7.1Mb
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installed size is 10.5Mb
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'LazyData' is specified without a 'data' directory
installed size is 114.6Mb
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installed size is 17.2Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 65.7Mb
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GNU make is a SystemRequirements.
installed size is  7.9Mb
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installed size is 57.9Mb
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GNU make is a SystemRequirements.
installed size is 196.8Mb
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GNU make is a SystemRequirements.
installed size is 48.3Mb
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installed size is 96.4Mb
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installed size is 32.9Mb
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Namespaces in Imports field not imported from:
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Malformed Description field: should contain one or more complete sentences.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<recently read> \mathbb 
                        
l.97 ...ong to a compact set of \eqn{\mathbb{R}}{}
                                                  .
! Undefined control sequence.
<recently read> \mathbb 
                        
l.161 ... to a compact set of \eqn{\mathbb{R}^2}{}
                                                  .
Namespace in Imports field not imported from: ‘rnaturalearthdata’
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installed size is 12.1Mb
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘preprocessCore’
'LazyData' is specified without a 'data' directory
installed size is  9.7Mb
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GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘SeqArray’
installed size is  7.9Mb
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'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
Namespaces in Imports field not imported from:
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installed size is  5.6Mb
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Namespace in Imports field not imported from: ‘Rcpp’
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Namespaces in Imports field not imported from:
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'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  7.6Mb
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installed size is 190.9Mb
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installed size is  7.9Mb
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Namespace in Imports field not imported from: ‘dplyr’
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'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
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Package suggested but not available for checking: ‘cmdstanr’
installed size is  5.6Mb
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Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
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Package suggested but not available for checking: ‘monocle’
Package unavailable to check Rd xrefs: ‘monocle’
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'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘reshape2’
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.6Mb
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installed size is  7.4Mb
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GNU make is a SystemRequirements.
accrualReport: multiple local function definitions for ‘gg’ with
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installed size is 28.7Mb
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GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
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'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
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Namespace in Imports field not imported from: ‘sf’
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Namespaces in Imports field not imported from:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
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Package suggested but not available for checking: ‘Rmpi’
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Warning: declared S3 method 'transform.trans_sax' not found
Warning: declared S3 method 'transform.trans_xsax' not found
See section ‘Generic functions and methods’ in the ‘Writing R
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GNU make is a SystemRequirements.
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'LazyData' is specified without a 'data' directory
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GNU make is a SystemRequirements.
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'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: ‘cmdstanr’
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'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
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installed size is  6.2Mb
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Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
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installed size is  7.3Mb
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'LazyData' is specified without a 'data' directory
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installed size is  6.3Mb
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'LazyData' is specified without a 'data' directory
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GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘Rmpi’
Package unavailable to check Rd xrefs: ‘Rmpi’
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘usethis’
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Package required but not available: ‘fmrs’

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installed size is 10.8Mb
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installed size is  6.9Mb
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installed size is  9.2Mb
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Package suggested but not available for checking: ‘INLA’
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
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installed size is 48.0Mb
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GNU make is a SystemRequirements.
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html_describe_con: multiple local function definitions for ‘g’ with
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  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   8.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 68.3Mb
  sub-directories of 1Mb or more:
    libs  67.7Mb
GNU make is a SystemRequirements.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   3.7Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘igraph’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   2.2Mb
    doc    2.3Mb
    help   1.1Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    dict   1.5Mb
    libs   5.1Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘hurricaneexposuredata’
Namespace in Imports field not imported from: ‘mapproj’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 44.0Mb
  sub-directories of 1Mb or more:
    libs  43.4Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘colourpicker’ ‘shiny’ ‘wordcloud2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘microViz’
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
    libs      1.8Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    extdata   5.7Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Package suggested but not available for checking: ‘webshot2’
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   6.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   1.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 38558 marked UTF-8 strings
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
Note: found 359 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘SparkR’
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    1.6Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.UCSC.hg38', 'BSgenome.Mmusculus.UCSC.mm10'
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘LTRCtrees’
Package unavailable to check Rd xrefs: ‘LTRCtrees’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘icd’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    libs  13.8Mb
Package suggested but not available for checking: ‘mixAK’
Namespaces in Imports field not imported from:
  ‘digest’ ‘purrr’ ‘tidyverse’
  All declared Imports should be used.
Note: found 10 marked UTF-8 strings
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   2.8Mb
'LazyData' is specified without a 'data' directory
installed size is 31.1Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  29.3Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rggobi’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘kableExtra’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Package suggested but not available for checking: ‘IFCdata’
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   4.5Mb
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘knitr’ ‘xtable’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  vendor/cigraph/vendor/glpk/api/mps.c:1297:19: warning: explicitly assigning value of variable of type 'GLPAIJ *' (aka 'struct GLPAIJ *') to itself [-Wself-assign]
  vendor/cigraph/vendor/glpk/draft/glpapi06.c:565:26: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  vendor/cigraph/vendor/glpk/draft/glpapi06.c:574:20: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  vendor/cigraph/vendor/glpk/draft/glpios01.c:224:17: warning: explicitly assigning value of variable of type 'IOSNPD *' (aka 'struct IOSNPD *') to itself [-Wself-assign]
  vendor/cigraph/vendor/glpk/misc/ks.c:428:14: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  vendor/cigraph/vendor/glpk/mpl/mpl6.c:687:17: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  vendor/cigraph/vendor/glpk/mpl/mpl6.c:854:20: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/igraph.Rcheck/00install.out’ for details.
installed size is 25.0Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    doc    1.2Mb
    help   2.8Mb
    libs  18.4Mb
File ‘igraph/libs/igraph.so’:
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
    Objects: ‘vendor/cigraph/vendor/glpk/env/stdout.o’,
      ‘vendor/cigraph/vendor/glpk/misc/mygmp.o’,
      ‘vendor/cigraph/vendor/glpk/mpl/mpl4.o’
  Found ‘_exit’, possibly from ‘exit’ (C)
    Object: ‘vendor/cigraph/vendor/glpk/proxy/main.o’
  Found ‘_printf’, possibly from ‘printf’ (C)
    Object: ‘vendor/cigraph/vendor/glpk/proxy/main.o’
  Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (C)
    Object: ‘vendor/cigraph/vendor/glpk/proxy/main.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    dlib-19.20   9.3Mb
    libs         4.3Mb
installed size is 31.3Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       3.7Mb
    extdata   1.0Mb
    include   3.0Mb
    libs     21.5Mb
installed size is 21.7Mb
  sub-directories of 1Mb or more:
    libs   10.5Mb
    share  10.2Mb
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    doc    1.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘accdata’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘lme4’ ‘reshape2’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
logLik:
  function(object, ...)
logLik.displacement:
  function(model, ...)

See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.

Found the following apparent S3 methods exported but not registered:
  logLik.displacement
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
S3 methods shown with full name in documentation object 'logLik.displacement':
  ‘logLik.displacement’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  10.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘INLA’
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   5.8Mb
Running examples in ‘inldata-Ex.R’ failed
The error most likely occurred in:

> ### Name: write_datasets
> ### Title: Write Package Datasets
> ### Aliases: write_datasets
> 
> ### ** Examples
> 
> dir <- tempfile("")
> write_datasets(
+   package = "inldata",
+   destdir = dir,
+   include = c("crs", "dl", "inl"),
+   pretty = FALSE,
+   quiet = TRUE
+ )
Error in parquet___WriterProperties___Builder__create() : 
  Cannot call parquet___WriterProperties___Builder__create(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries. 
Calls: write_datasets ... <Anonymous> -> parquet___WriterProperties___Builder__create
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Namespace in Imports field not imported from: ‘splines2’
  All declared Imports should be used.
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is 30.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  28.7Mb
Namespace in Imports field not imported from: ‘moonBook’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘curl’ ‘readxl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    doc   9.9Mb
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/intrinsicFRP.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘surveyspec’
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rhdf5’
File ‘iotools/libs/iotools.so’:
  Found non-API calls to R: ‘R_GetConnection’, ‘R_ReadConnection’,
    ‘R_WriteConnection’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 46 marked UTF-8 strings
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  `expected`: 6
  ── Failure ('test-dday.R:10:3'): dday works ────────────────────────────────────
  dday(df, "2023-08-01", d = 1, x = "x") (`actual`) not identical to 13 (`expected`).
  
    `actual`:  0
  `expected`: 13
  ── Failure ('test-ytd.R:12:3'): ytd works ──────────────────────────────────────
  ytd(df, "2023-08-01", x = "x") (`actual`) not equal to dday(df, "2023-08-01", x = "x") (`expected`).
  
    `actual`: 10
  `expected`:  0
  
  [ FAIL 5 | WARN 0 | SKIP 0 | PASS 45 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    libs  12.2Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘seqinr’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
Package suggested but not available for checking: ‘Rmpi’
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘glmnet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 12 marked UTF-8 strings
Note: found 104 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
installed size is 62.8Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    2.3Mb
    libs  57.6Mb
GNU make is a SystemRequirements.
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs  11.8Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
Note: found 58 marked UTF-8 strings
Package suggested but not available for checking: ‘locClass’
Packages suggested but not available for checking: 'gurobi', 'cplexAPI'
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘dplyr’ ‘magrittr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 18.1Mb
  sub-directories of 1Mb or more:
    art_profiles   1.5Mb
    libs          15.8Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘fBasics’ ‘reshape’ ‘tidyr’ ‘utils’
  All declared Imports should be used.
Note: found 2261 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 1984 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘grid’ ‘mcmcplots’ ‘tidyverse’
  All declared Imports should be used.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/JavaGD.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    htmlwidgets   5.7Mb
installed size is 90.5Mb
  sub-directories of 1Mb or more:
    libs  89.1Mb
GNU make is a SystemRequirements.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
    libs      1.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is 32.7Mb
  sub-directories of 1Mb or more:
    libs  32.3Mb
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   5.5Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    i18n   6.5Mb
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   4.2Mb
Package which this enhances but not available for checking: ‘remMap’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘doParallel’
  All declared Imports should be used.
Note: found 176 marked UTF-8 strings
Package required but not available: ‘scran’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is 34.2Mb
  sub-directories of 1Mb or more:
    libs  32.7Mb
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    libs  16.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   4.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    examples      2.8Mb
    htmlwidgets   1.1Mb
    www           2.7Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Superpower’ ‘pwr’ ‘shinydashboard’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘gifski’
  All declared Imports should be used.
Package required but not available: ‘pbdMPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  14.3Mb
Namespaces in Imports field not imported from:
  ‘EQL’ ‘univariateML’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘lme4’ ‘metafor’ ‘nlme’
  All declared Imports should be used.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    help   8.0Mb
'LazyData' is specified without a 'data' directory
apparently using $(BLAS_LIBS) without following $(FLIBS) in ‘src/Makevars’
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    libs  16.1Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Biostrings’ ‘Rsamtools’ ‘rtracklayer’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘fitdistrplus’ ‘plotly’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘Instruction_of_functions_of_R_package_KINSIMU.Rnw’ using Sweave
Error: processing vignette 'Instruction_of_functions_of_R_package_KINSIMU.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'Instruction_of_functions_of_R_package_KINSIMU.tex' failed.
LaTeX errors:
! LaTeX Error: Command \gather already defined.
               Or name \end... illegal, see p.192 of the manual.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
! Emergency stop.
 ...                                              
                                                  
l.1560 }
        
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘Instruction_of_functions_of_R_package_KINSIMU.Rnw’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘rkward’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RGeostats’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Errors in running code in vignettes:
when running code in ‘knit_expand.Rmd’
  ...
</html>
> src = lapply(names(mtcars)[-1], function(i) {
+     knit_expand(text = c("# Regression on {{i}}", "```{r lm-{{i}}}", 
+         "lm(mpg~{{i}}, data= ..." ... [TRUNCATED] 

> res = knit_child(text = unlist(src))

  When sourcing ‘knit_expand.R’:
Error: character argument expected
Execution halted
when running code in ‘docco-classic.Rmd’
  ...

> x[i] = "knitr::rocco"

> library(knitr)

> cat(knit_child(text = x, quiet = TRUE), sep = "\n")

  When sourcing ‘docco-classic.R’:
Error: character argument expected
Execution halted

  ‘knitr-refcard.Rmd’ using ‘UTF-8’... [0s/0s] OK
  ‘datatables.Rmd’ using ‘UTF-8’... [0s/0s] OK
  ‘knit_expand.Rmd’ using ‘UTF-8’... failed
  ‘knit_print.Rmd’ using ‘UTF-8’... [0s/0s] OK
  ‘knitr-html.Rhtml’ using ‘UTF-8’... [0s/0s] OK
  ‘knitr-intro.Rmd’ using ‘UTF-8’... [0s/0s] OK
  ‘knitr-markdown.Rmd’ using ‘UTF-8’... [0s/0s] OK
  ‘docco-classic.Rmd’ using ‘UTF-8’... failed
  ‘docco-linear.Rmd’ using ‘UTF-8’... [0s/0s] OK
Namespaces in Imports field not imported from:
  ‘FNN’ ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘psycho’ ‘rhandsontable’
  ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   4.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Packages suggested but not available for checking:
  'koRpus.lang.de', 'koRpus.lang.es', 'koRpus.lang.fr',
  'koRpus.lang.it', 'koRpus.lang.nl', 'koRpus.lang.pt',
  'koRpus.lang.ru'

Package which this enhances but not available for checking: ‘rkward’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs  10.8Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘robustbase’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R   5.1Mb
Namespace in Imports field not imported from: ‘stringr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   8.2Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
GNU make is a SystemRequirements.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.5Mb
'LazyData' is specified without a 'data' directory
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   5.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    doc    1.7Mb
    help   1.1Mb
Note: found 6 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘mixAK’
Package unavailable to check Rd xrefs: ‘mixAK’
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   6.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘doParallel’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘SnowballC’ ‘chinese.misc’ ‘dplyr’ ‘factoextra’ ‘glasso’
  ‘highcharter’ ‘htmlwidgets’ ‘ldatuning’ ‘qgraph’ ‘quanteda’ ‘rvest’
  ‘shinyBS’ ‘shinyWidgets’ ‘shinyalert’ ‘shinybusy’ ‘shinycssloaders’
  ‘shinydashboard’ ‘shinyjs’ ‘stringr’ ‘textmineR’ ‘textplot’ ‘tidyr’
  ‘topicmodels’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘SnowballC’ ‘beepr’ ‘broom’ ‘chinese.misc’ ‘dplyr’ ‘highcharter’
  ‘htmlwidgets’ ‘ldatuning’ ‘parallel’ ‘plotly’ ‘purrr’ ‘quanteda’
  ‘shinyBS’ ‘shinyWidgets’ ‘shinyalert’ ‘shinycssloaders’ ‘shinyjs’
  ‘stringr’ ‘textmineR’ ‘tidyr’ ‘tidytext’ ‘topicmodels’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘devtools’ ‘reticulate’ ‘tensorflow’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is 26.1Mb
  sub-directories of 1Mb or more:
    libs  24.8Mb
Note: found 75 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘htmlwidgets’ ‘jsonlite’ ‘sf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘leaflet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 53.4Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs  49.2Mb
GNU make is a SystemRequirements.
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    libs  15.7Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   6.0Mb
installed size is 46.2Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs  43.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘LFDREmpiricalBayes.Rnw’ using Sweave

Error: processing vignette 'LFDREmpiricalBayes.Rnw' failed with diagnostics:
 chunk 4 (label = generating artificial SNPs) 
Error in library(LFDR.MLE) : there is no package called ‘LFDR.MLE’

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

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

Error: Vignette re-building failed.
Execution halted
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs  10.5Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘knitr’ ‘purrr’ ‘rmarkdown’
  All declared Imports should be used.
installed size is 93.7Mb
  sub-directories of 1Mb or more:
    libs  92.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Note: found 22 marked UTF-8 strings
installed size is 43.2Mb
  sub-directories of 1Mb or more:
    libs  43.0Mb
'LazyData' is specified without a 'data' directory
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    R         1.0Mb
    doc       1.0Mb
    extdata   1.2Mb
    libs      9.0Mb
Packages suggested but not available for checking:
  'gWidgets', 'gWidgetsRGtk2', 'RGtk2'
Namespaces in Imports field not imported from:
  ‘curl’ ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    2.1Mb
    libs   1.5Mb
installed size is 62.0Mb
  sub-directories of 1Mb or more:
    libs  61.3Mb
'LazyData' is specified without a 'data' directory
Note: found 7 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘data.table’ ‘e1071’ ‘fastmatch’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Invalid citation information in ‘inst/CITATION’:
  Error in format.default(meta$Date, "%Y"): invalid 'trim' argument
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 32 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘e1071’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 27.3Mb
  sub-directories of 1Mb or more:
    R          1.5Mb
    doc        1.6Mb
    libs      22.1Mb
    testdata   1.3Mb
installed size is 56.7Mb
  sub-directories of 1Mb or more:
    libs  55.7Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘mnormt’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Running ‘tinytest.R’ [3s/3s]
Running the tests in ‘tests/tinytest.R’ failed.
Last 13 lines of output:
  test_spl3D.R..................   11 tests [0;32mOK[0m 
  test_spl3D.R..................   12 tests [0;32mOK[0m 
  test_spl3D.R..................   13 tests [0;32mOK[0m 
  test_spl3D.R..................   14 tests [0;32mOK[0m 
  test_spl3D.R..................   15 tests [0;32mOK[0m 
  test_spl3D.R..................   16 tests [0;32mOK[0m 
  test_spl3D.R..................   16 tests [0;32mOK[0m 
  test_spl3D.R..................   16 tests [0;32mOK[0m 
  test_spl3D.R..................   17 tests [0;32mOK[0m [0;34m0.3s[0m
  ----- FAILED[data]: test_GLMM.R<19--19>
   call| expect_equal_to_reference(obj1, "GLMMFull", check.attributes = FALSE)
   diff| current does not match target read from GLMMFull
   diff| Component "family": Length mismatch: comparison on first 12 components
  Error: 1 out of 145 tests failed
  Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R              2.0Mb
    doc-software   2.4Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
Namespace in Imports field not imported from: ‘shinyjs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 64.9Mb
  sub-directories of 1Mb or more:
    libs  64.4Mb
Namespace in Imports field not imported from: ‘checkmate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 33.7Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  31.7Mb
Running examples in ‘localsolver-Ex.R’ failed
The error most likely occurred in:

> ### Name: add.output.expr
> ### Title: Add expression to output of ls.problem.
> ### Aliases: add.output.expr
> 
> ### ** Examples
> 
> model.text.lsp <- lsp.model.example('extdata/knapsack.txt')
> lsp <- ls.problem(model.text.lsp)
sh: localsolver: command not found
Error in ls.problem(model.text.lsp) : 
  has.localsolver(ls.path) is not TRUE
Calls: ls.problem -> stopifnot
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘localsolver.Rmd’ using knitr
sh: localsolver: command not found
Quitting from lines 66-68 (localsolver.Rmd) 
Error: processing vignette 'localsolver.Rmd' failed with diagnostics:
has.localsolver(ls.path) is not TRUE
--- failed re-building ‘localsolver.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘lestat’
  All declared Imports should be used.
installed size is 27.3Mb
  sub-directories of 1Mb or more:
    libs  27.1Mb
Package suggested but not available for checking: ‘EnsDb.Hsapiens.v75’
Note: found 12 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 20.2Mb
  sub-directories of 1Mb or more:
    libs  18.5Mb
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/longclust.Rcheck/00install.out’ for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
    libs   1.6Mb
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘QSutils’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘scio’
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
    libs      1.0Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 52.7Mb
  sub-directories of 1Mb or more:
    libs  50.7Mb
Package suggested but not available for checking: ‘miceadds’
Note: found 55 marked UTF-8 strings
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    libs  15.6Mb
'LazyData' is specified without a 'data' directory
installed size is 50.0Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs  47.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error: package or namespace load failed for ‘LSTbook’:
 .onLoad failed in loadNamespace() for 'LSTbook', details:
  call: loadNamespace(name)
  error: there is no package called ‘ggformula’
Execution halted

It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘rpostgis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.9Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   1.9Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R   5.0Mb
'LazyData' is specified without a 'data' directory
installed size is 24.4Mb
  sub-directories of 1Mb or more:
    libs  24.2Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘e1071’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘orthogene’
Package unavailable to check Rd xrefs: ‘orthogene’
Package suggested but not available for checking: ‘rnaturalearthhires’
Namespace in Imports field not imported from: ‘R.utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘rlang’ ‘torch’
  All declared Imports should be used.
installed size is 31.6Mb
  sub-directories of 1Mb or more:
    libs  31.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘quitte’
Package suggested but not available for checking: ‘SeqArray’
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is 55.5Mb
  sub-directories of 1Mb or more:
    doc    6.3Mb
    libs  48.5Mb
'LazyData' is specified without a 'data' directory
installed size is 26.4Mb
  sub-directories of 1Mb or more:
    libs  25.0Mb
Packages suggested but not available for checking: 'pdInfoBuilder', 'oligo'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘BiocCheck’
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    data   2.3Mb
    libs   5.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
Namespaces in Imports field not imported from:
  ‘cli’ ‘nomnoml’
  All declared Imports should be used.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
Note: found 55 marked UTF-8 strings
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.5Mb
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Note: found 3058 marked UTF-8 strings
Note: found 11396 marked UTF-8 strings
installed size is 33.5Mb
  sub-directories of 1Mb or more:
    mapdata  33.4Mb
installed size is 22.2Mb
  sub-directories of 1Mb or more:
    data          1.3Mb
    doc           1.6Mb
    htmlwidgets   3.5Mb
    libs         15.3Mb
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    data   2.4Mb
    libs   4.7Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘pbmcapply’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   2.0Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
GNU make is a SystemRequirements.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc   7.4Mb
Note: found 5210 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    examples   2.7Mb
    libs      11.3Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.4Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘marssTMB’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.NCBI.GRCh38', 'wiggleplotr'
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
installed size is 49.2Mb
  sub-directories of 1Mb or more:
    libs  48.9Mb
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/MASS.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   8.8Mb
Package suggested but not available for checking: ‘gurobi’
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   3.3Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rrelaxiv’
'LazyData' is specified without a 'data' directory
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    libs  13.1Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   9.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
GNU make is a SystemRequirements.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/Matrix.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 18 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   3.9Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘lars’ ‘methods’ ‘parallel’ ‘smoothmest’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs  12.2Mb
Namespace in Imports field not imported from: ‘boot.heterogeneity’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
installed size is 34.3Mb
  sub-directories of 1Mb or more:
    libs  33.1Mb
'LazyData' is specified without a 'data' directory
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    libs  16.7Mb
'LazyData' is specified without a 'data' directory
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs  15.9Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc   6.8Mb
Package suggested but not available for checking: ‘cmdstanr’
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘psych’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
Package suggested but not available for checking: ‘RGtk2’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘glmnet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   5.3Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘datasets’ ‘dplyr’ ‘psych’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
installed size is 64.1Mb
  sub-directories of 1Mb or more:
    libs  62.7Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 35.6Mb
  sub-directories of 1Mb or more:
    libs  34.5Mb
'LazyData' is specified without a 'data' directory
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    libs  18.3Mb
ADPopSel: no visible global function definition for ‘%dorng%’
ADRand: no visible global function definition for ‘%dorng%’
ADSSMod: no visible global function definition for ‘%dorng%’
ADTreatSel: no visible global function definition for ‘%dorng%’
ClustRand: no visible global function definition for ‘%dorng%’
EventPred: no visible global function definition for ‘%dorng%’
FutRuleNCores: no visible global function definition for ‘%dorng%’
MultAdj1NCores: no visible global function definition for ‘%dorng%’
MultAdj2NCores: no visible global function definition for ‘%dorng%’
MultAdj3NCores: no visible global function definition for ‘%dorng%’
Undefined global functions or variables:
  %dorng%
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 155.3Mb
  sub-directories of 1Mb or more:
    libs  153.7Mb
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   3.1Mb
Namespace in Imports field not imported from: ‘urca’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘merlin.Rmd’ using rmarkdown

Execution halted

* checking PDF version of manual ...* using check arguments '--no-clean-on-error '
installed size is 21.2Mb
  sub-directories of 1Mb or more:
    libs  20.1Mb
'LazyData' is specified without a 'data' directory
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   5.4Mb
Namespace in Imports field not imported from: ‘gt’
  All declared Imports should be used.
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
installed size is 107.2Mb
  sub-directories of 1Mb or more:
    libs  106.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘e1071’ ‘gbm’ ‘ggplot2’ ‘graphics’ ‘randomForest’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    help   2.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘BiocManager’ ‘DT’ ‘GEOmetadb’ ‘RMySQL’ ‘RSQLite’ ‘gplots’ ‘pheatmap’
  ‘readr’
  All declared Imports should be used.
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    data       3.0Mb
    examples  10.3Mb
Packages suggested but not available for checking:
  'hgu133a.db', 'hgu95av2.db'
Namespace in Imports field not imported from: ‘progress’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lmerTest’
  All declared Imports should be used.
installed size is 20.4Mb
  sub-directories of 1Mb or more:
    libs  20.0Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ade4’ ‘dendextend’ ‘ggforce’ ‘ggrepel’ ‘stringr’ ‘tidyverse’
  All declared Imports should be used.
installed size is 58.9Mb
  sub-directories of 1Mb or more:
    libs  58.5Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘metadat’
  All declared Imports should be used.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   2.0Mb
    libs   2.7Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
installed size is 27.3Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    2.8Mb
    libs  20.6Mb
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   6.5Mb
Package required but not available: ‘qusage’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘boot’ ‘energy’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 19.7Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  17.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘structSSI’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'DAPAR', 'ProteoMM'
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘dada2’
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Package required but not available: ‘microbiome’

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.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘microcontax.data’
Package unavailable to check Rd xrefs: ‘microcontax.data’
Namespaces in Imports field not imported from:
  ‘DT’ ‘ggiraph’ ‘ggplot2’ ‘grid’ ‘gtools’ ‘scales’ ‘shinyBS’
  ‘shinyWidgets’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
installed size is 20.1Mb
  sub-directories of 1Mb or more:
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    lib    8.8Mb
    libs   4.4Mb
Found the following apparent S3 methods exported but not registered:
  plot.icss print.icss print.micss
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘midfielddata’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Package suggested but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘FactoMineR’ ‘softImpute’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
'LazyData' is specified without a 'data' directory
installed size is 22.3Mb
  sub-directories of 1Mb or more:
    libs  22.2Mb
Package required but not available: ‘InteractiveComplexHeatmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 116.7Mb
  sub-directories of 1Mb or more:
    libs  116.0Mb
Namespaces in Imports field not imported from:
  ‘pracma’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   6.3Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'mixAK', 'BRugs'
Package unavailable to check Rd xrefs: ‘mixAK’
Package required but not available: ‘dada2’

Packages suggested but not available for checking: 'ANCOMBC', 'mia'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc       2.4Mb
    extdata   1.2Mb
    libs      1.6Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Packages suggested but not available for checking:
  'karyoploteR', 'regioneR'
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    libs  13.0Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Package which this enhances but not available for checking: ‘pbdMPI’
Package required but not available: ‘scran’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
Namespaces in Imports field not imported from:
  ‘ashr’ ‘fdrtool’
  All declared Imports should be used.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   4.3Mb
'LazyData' is specified without a 'data' directory
Warning: declared S3 method 'smooth.construct.unc_pcre.smooth.spec' not found
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘reticulate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ConfusionTableR’ ‘OddsPlotty’ ‘caret’ ‘dplyr’ ‘ggplot2’ ‘parsnip’
  ‘ranger’ ‘recipes’ ‘rsample’ ‘varhandle’ ‘workflows’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'ueadata1', 'ueadata2', 'ueadata3', 'ueadata4', 'ueadata5',
  'ueadata6', 'ueadata7', 'ueadata8'
installed size is 237.0Mb
  sub-directories of 1Mb or more:
    include    9.6Mb
    libs     226.9Mb
Namespaces in Imports field not imported from:
  ‘caret’ ‘randomForest’
  All declared Imports should be used.
Running examples in ‘mlr3spatiotempcv-Ex.R’ failed
The error most likely occurred in:

> ### Name: mlr_resamplings_repeated_spcv_knndm
> ### Title: (CAST) Repeated K-fold Nearest Neighbour Distance Matching
> ### Aliases: mlr_resamplings_repeated_spcv_knndm
> ###   ResamplingRepeatedSpCVKnndm
> 
> ### ** Examples
> 
> library(mlr3)
> library(mlr3spatial)

Attaching package: ‘mlr3spatial’

The following objects are masked from ‘package:mlr3spatiotempcv’:

    TaskClassifST, TaskRegrST, as_task_classif_st,
    as_task_classif_st.DataBackend, as_task_classif_st.TaskClassifST,
    as_task_classif_st.data.frame, as_task_classif_st.sf,
    as_task_regr_st, as_task_regr_st.DataBackend,
    as_task_regr_st.TaskClassifST, as_task_regr_st.TaskRegrST,
    as_task_regr_st.data.frame, as_task_regr_st.sf

> set.seed(42)
> simarea = list(matrix(c(0, 0, 0, 100, 100, 100, 100, 0, 0, 0), ncol = 2, byrow = TRUE))
> simarea = sf::st_polygon(simarea)
> train_points = sf::st_sample(simarea, 1000, type = "random")
> train_points = sf::st_as_sf(train_points)
> train_points$target = as.factor(sample(c("TRUE", "FALSE"), 1000, replace = TRUE))
> pred_points = sf::st_sample(simarea, 1000, type = "regular")
> 
> task = mlr3spatial::as_task_classif_st(sf::st_as_sf(train_points), "target", positive = "TRUE")
> 
> cv_knndm = rsmp("repeated_spcv_knndm", predpoints = pred_points, repeats = 2)
> cv_knndm$instantiate(task)
Error in CAST::knndm(tpoints = points, modeldomain = self$param_set$values$modeldomain,  : 
  unused argument (predpoints = self$param_set$values$predpoints)
Calls: <Anonymous> ... .__ResamplingRepeatedSpCVKnndm__.sample -> map -> lapply -> FUN
Execution halted
Running ‘testthat.R’ [44s/30s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  • 2-autoplot/sptcvcstf-2d-space-var-fold-1-2.svg
  • 2-autoplot/sptcvcstf-2d-space-var-fold-1.svg
  • 2-autoplot/sptcvcstf-2d-time-var-fold-1-2-rep-2.svg
  • 2-autoplot/sptcvcstf-2d-time-var-fold-1-2-sample-fold-n.svg
  • 2-autoplot/sptcvcstf-2d-time-var-fold-1-2.svg
  • 2-autoplot/sptcvcstf-2d-time-var-fold-1-rep-2.svg
  • 2-autoplot/sptcvcstf-2d-time-var-fold-1-sample-fold-n.svg
  • 2-autoplot/sptcvcstf-2d-time-var-fold-1.svg
  • 2-autoplot/sptcvcstf-2d-time-var-sample-fold-n.svg
  • 2-autoplot/sptcvcstf-3d-time-var-fold-1-2-sample-fold-n.svg
  • 2-autoplot/sptcvcstf-3d-time-var-fold-1-2.svg
  • 2-autoplot/sptcvcstf-3d-time-var-fold-1-sample-fold-n.svg
  • autoplot_buffer/spcvbuffer-fold-1-2.svg
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Rmpi’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    data   2.3Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
'LazyData' is specified without a 'data' directory
installed size is 35.8Mb
  sub-directories of 1Mb or more:
    libs  35.3Mb
installed size is 22.1Mb
  sub-directories of 1Mb or more:
    libs  21.4Mb
'LazyData' is specified without a 'data' directory
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    images   1.1Mb
    shiny   14.5Mb
Namespaces in Imports field not imported from:
  ‘Cairo’ ‘DT’ ‘XML’ ‘caTools’ ‘data.table’ ‘dplyr’ ‘ggplot2’
  ‘htmltools’ ‘leaflet’ ‘lubridate’ ‘plotly’ ‘shinyjs’ ‘stringr’ ‘xts’
  ‘zoo’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘datasets’ ‘doParallel’ ‘parallel’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs  15.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 20.7Mb
  sub-directories of 1Mb or more:
    libs  20.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 110.0Mb
  sub-directories of 1Mb or more:
    libs  108.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    libs  15.3Mb
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘e1071’ ‘nnet’ ‘shiny’ ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'doMPI', 'alstructure'

Package which this enhances but not available for checking: ‘MoBPSmaps’
Packages required but not available:
  'plyranges', 'RaggedExperiment', 'MultiAssayExperiment', 'ggbio'

Packages suggested but not available for checking:
  'ArchR', 'motifmatchr', 'TxDb.Hsapiens.UCSC.hg38.refGene',
  'BSgenome.Hsapiens.UCSC.hg19', 'chromVAR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
Namespaces in Imports field not imported from:
  ‘DALEX’ ‘DT’ ‘auditor’ ‘breakDown’ ‘drifter’ ‘svglite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Note: found 18 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
Note: found 5238 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
'LazyData' is specified without a 'data' directory
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    1.7Mb
    libs   4.7Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    htmlwidgets  14.7Mb
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   7.1Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘caret’ ‘ggformula’ ‘knitr’ ‘testthat’ ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘NlcOptim’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs     3.0Mb
    raster   2.2Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R   2.0Mb
'LazyData' is specified without a 'data' directory
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
'LazyData' is specified without a 'data' directory
installed size is 68.9Mb
  sub-directories of 1Mb or more:
    libs  68.5Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs  12.7Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Biostrings’
Package unavailable to check Rd xrefs: ‘Biostrings’
'LazyData' is specified without a 'data' directory
Note: found 75 marked UTF-8 strings
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
'LazyData' is specified without a 'data' directory
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    data   4.5Mb
    libs   3.5Mb
installed size is 45.2Mb
  sub-directories of 1Mb or more:
    libs  44.8Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyselect’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R   6.1Mb
Namespace in Imports field not imported from: ‘ranger’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following apparent S3 methods exported but not registered:
  plot.prevalence.msm plot.survfit.msm
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Namespaces in Imports field not imported from:
  ‘datasets’ ‘grDevices’ ‘graphics’ ‘iterators’ ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘markdown’ ‘methods’ ‘vctrs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘mtvc-Ex.R’ failed
The error most likely occurred in:

> ### Name: mtvc
> ### Title: (mtvc) Multiple Time Varying Covariates
> ### Aliases: mtvc
> 
> ### ** Examples
> 
> data(simwide)
> cp.dataframe=mtvc(data=simwide,
+ origin='1970-01-01',
+ dates=c(FIRST_CHRONIC,FIRST_ACUTE,FIRST_RELAPSE),
+ complications=c(CHRONIC,ACUTE,RELAPSE),
+ start=DATETRAN,
+ stop=DLASTSE,
+ event=EVENT)
Error in `mutate()`:
ℹ In argument: `FIRST_CHRONIC = (structure(function (..., .x = ..1, .y =
  ..2, . = ..1) ...`.
Caused by error in `as.Date.numeric()`:
! 'origin' must be supplied
Backtrace:
     ▆
  1. ├─mtvc::mtvc(...)
  2. │ └─data %>% ungroup() %>% mutate(id = row_number()) %>% ...
  3. ├─dplyr::mutate_at(...)
  4. │ ├─dplyr::mutate(.tbl, !!!funs)
  5. │ └─dplyr:::mutate.data.frame(.tbl, !!!funs)
  6. │   └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
  7. │     ├─base::withCallingHandlers(...)
  8. │     └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
  9. │       └─mask$eval_all_mutate(quo)
 10. │         └─dplyr (local) eval()
 11. ├─mtvc (local) `<inln_cl_>`(FIRST_CHRONIC)
 12. │ └─rlang::eval_bare(`_quo`, base::parent.frame())
 13. ├─rlang (local) as.Date(ifelse(is.na(.), as.Date(origin), as.Date(.)))
 14. ├─base::as.Date(ifelse(is.na(.), as.Date(origin), as.Date(.)))
 15. ├─base::as.Date.numeric(ifelse(is.na(.), as.Date(origin), as.Date(.)))
 16. │ └─base::stop("'origin' must be supplied")
 17. └─base::.handleSimpleError(...)
 18.   └─dplyr (local) h(simpleError(msg, call))
 19.     └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
Execution halted
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    9. │       └─mask$eval_all_mutate(quo)
   10. │         └─dplyr (local) eval()
   11. ├─mtvc (local) `<inln_cl_>`(FIRST_CHRONIC)
   12. │ └─rlang::eval_bare(`_quo`, base::parent.frame())
   13. ├─rlang (local) as.Date(ifelse(is.na(.), as.Date(origin), as.Date(.)))
   14. ├─base::as.Date(ifelse(is.na(.), as.Date(origin), as.Date(.)))
   15. ├─base::as.Date.numeric(ifelse(is.na(.), as.Date(origin), as.Date(.)))
   16. │ └─base::stop("'origin' must be supplied")
   17. └─base::.handleSimpleError(...)
   18.   └─dplyr (local) h(simpleError(msg, call))
   19.     └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘capushe’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
'LazyData' is specified without a 'data' directory
Found the following apparent S3 methods exported but not registered:
  plot.TetraDualStatis summary.TetraDualStatis
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   7.2Mb
'LazyData' is specified without a 'data' directory
Package required but not available: ‘GFDmcv’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespace in Imports field not imported from: ‘plsgenomics’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
'LazyData' is specified without a 'data' directory
installed size is 106.9Mb
  sub-directories of 1Mb or more:
    libs  106.6Mb
installed size is 271.1Mb
  sub-directories of 1Mb or more:
    R       2.0Mb
    doc     4.4Mb
    libs  264.0Mb
GNU make is a SystemRequirements.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Package suggested but not available for checking: ‘rrelaxiv’
installed size is 35.8Mb
  sub-directories of 1Mb or more:
    libs  35.5Mb
GNU make is a SystemRequirements.
Error(s) in re-building vignettes:
--- re-building ‘multipol.Rnw’ using Sweave
Loading required package: multipol
Loading required package: abind

Attaching package: ‘multipol’

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

    deriv

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

    single

Loading required package: polynom
Error: processing vignette 'multipol.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'multipol.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 657 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘multipol.Rnw’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    help   2.2Mb
    libs   2.1Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘poweRlaw’ ‘rmutil’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
Note: found 6 marked UTF-8 strings
Error(s) in re-building vignettes:
  ...
--- re-building ‘cias.Rnw’ using Sweave

Attaching package: ‘multivator’

The following objects are masked from ‘package:base’:

    levels, rbind

--- finished re-building ‘cias.Rnw’

--- re-building ‘multivator.Rnw’ using Sweave
Error: processing vignette 'multivator.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'multivator.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 657 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'multivator.Rnw'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    libs  11.8Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘grDevices’ ‘knitr’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    java   2.5Mb
    libs   6.5Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘rTubeDB’
Package unavailable to check Rd xrefs: ‘rTubeDB’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
Namespaces in Imports field not imported from:
  ‘glmnet’ ‘mlr3learners’ ‘rpart’
  All declared Imports should be used.
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    extdata  16.2Mb
'LazyData' is specified without a 'data' directory
installed size is 26.0Mb
  sub-directories of 1Mb or more:
    data     1.9Mb
    libs    22.9Mb
    models   1.1Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [8s/9s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  • gg-miss-case/gg-miss-case-plot-show-pct.svg
  • gg-miss-case/gg-miss-case-sort-show-pct.svg
  • gg-miss-case/gg-miss-case-sort.svg
  • gg-miss-case/gg-miss-case.svg
  • gg-miss-fct/gg-miss-fct.svg
  • gg-miss-span/gg-miss-span-group.svg
  • gg-miss-span/gg-miss-span.svg
  • gg-miss-var-cumsum/gg-miss-var-cumsum.svg
  • gg-miss-var-plot/gg-miss-var-group-pct.svg
  • gg-miss-var-plot/gg-miss-var-pct.svg
  • gg-miss-var-plot/gg-miss-var-plot-group.svg
  • gg-miss-var-plot/gg-miss-var.svg
  • gg-miss-which/gg-miss-which.svg
  Error: Test failures
  Execution halted
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs  10.3Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘spatialClust’
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    doc    1.7Mb
Namespace in Imports field not imported from: ‘tuneR’
  All declared Imports should be used.
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    6.5Mb
    libs   5.1Mb
GNU make is a SystemRequirements.
Note: found 140 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
Namespaces in Imports field not imported from:
  ‘glmnet’ ‘rrpack’
  All declared Imports should be used.
Package suggested but not available for checking: ‘sSeq’
Package unavailable to check Rd xrefs: ‘sSeq’
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘bookdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Deriv’ ‘compiler’ ‘stringi’
  All declared Imports should be used.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   4.2Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘fields’ ‘mvtnorm’
  All declared Imports should be used.
Note: found 7332 marked UTF-8 strings
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
installed size is 24.8Mb
  sub-directories of 1Mb or more:
    libs  23.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘igraph’ ‘rlang’ ‘tidyselect’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   5.5Mb
installed size is 21.0Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs  17.3Mb
Package suggested but not available for checking: ‘fastshp’
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   4.9Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   5.5Mb
Packages required and available but unsuitable versions: 'stats', 'utils'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespaces in Imports field not imported from:
  ‘mgcv’ ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 243.5Mb
  sub-directories of 1Mb or more:
    libs  242.8Mb
GNU make is a SystemRequirements.
Note: found 2 marked Latin-1 strings
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   7.8Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'ANTsR', 'ITKR', 'extrantsr', 'MNITemplate', 'RAVEL', 'neurodata'
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘xml2’
  All declared Imports should be used.
Note: found 318 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘curl’ ‘mathjaxr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘nflfastR’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages which this enhances but not available for checking:
  'NGCHMDemoData', 'NGCHMSupportFiles'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘NHSRdatasets’ ‘grid’ ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rJava’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.0Mb
Note: found 24 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 43.2Mb
  sub-directories of 1Mb or more:
    CppCode        3.5Mb
    R              8.1Mb
    classic-bugs   1.5Mb
    include       11.5Mb
    libs          17.9Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc       4.0Mb
    extdata   1.8Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Package which this enhances but not available for checking: ‘jpndistrict’
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘rjson’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 4 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
installed size is 19.5Mb
  sub-directories of 1Mb or more:
    libs  18.0Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc       1.2Mb
    extdata   3.7Mb
Namespaces in Imports field not imported from:
  ‘devtools’ ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
Package suggested but not available for checking: ‘doMPI’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘hurricaneexposuredata’
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘choroplethr’ ‘choroplethrMaps’ ‘data.table’ ‘forcats’
  ‘hurricaneexposure’ ‘plyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘crayon’ ‘digest’ ‘hash’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘e1071’ ‘pROC’ ‘purrr’ ‘randomForest’ ‘rlang’
  All declared Imports should be used.
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   5.1Mb
    mods   3.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘e1071’ ‘glmnet’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs       3.1Mb
    tinytest   1.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Rmpi’
Found the following apparent S3 methods exported but not registered:
  print.fkk.test
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘xgboost’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
Namespaces in Imports field not imported from:
  ‘forecast’ ‘rlang’ ‘tsibble’ ‘viridis’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘pedtools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 20.7Mb
  sub-directories of 1Mb or more:
    doc    5.3Mb
    libs  14.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   6.4Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘httr’
  All declared Imports should be used.
Note: found 7 marked UTF-8 strings
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R         2.0Mb
    doc       5.7Mb
    extdata   1.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R            1.6Mb
    test_files   4.2Mb
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    data   1.0Mb
    doc    1.7Mb
    help   3.4Mb
    libs   3.2Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    libs   1.9Mb
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
Namespaces in Imports field not imported from:
  ‘caret’ ‘e1071’ ‘ggthemes’ ‘mlbench’ ‘rmarkdown’ ‘tidymodels’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘graphics’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
installed size is 99.2Mb
  sub-directories of 1Mb or more:
    libs  98.2Mb
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   6.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gt’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 842 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘crayon’ ‘testthat’
  All declared Imports should be used.
Package suggested but not available for checking: ‘cmdstanr’
installed size is 45.9Mb
  sub-directories of 1Mb or more:
    libs  44.0Mb
GNU make is a SystemRequirements.
installed size is 42.3Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  40.1Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘e1071’ ‘fs’ ‘pdp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    libs  16.2Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘safer’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   1.6Mb
Note: found 34 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘randomForest’ ‘ranger’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘glue’ ‘httpcode’ ‘httr’ ‘jsonlite’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    exampledata   1.5Mb
    libs          3.5Mb
GNU make is a SystemRequirements.
installed size is 31.2Mb
  sub-directories of 1Mb or more:
    libs   20.9Mb
    share  10.2Mb
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   7.0Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
Note: found 2524 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 200.9Mb
  sub-directories of 1Mb or more:
    R         3.1Mb
    data      1.4Mb
    libs    189.3Mb
    models    4.7Mb
GNU make is a SystemRequirements.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    java     1.2Mb
    models   6.0Mb
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installed size is  5.9Mb
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installed size is  5.9Mb
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Note: found 167 marked UTF-8 strings
installed size is 12.1Mb
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installed size is  6.9Mb
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installed size is 37.3Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Package required but not available: ‘mixAK’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘gurobi’
installed size is  8.3Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
Package which this enhances but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
Package suggested but not available for checking: ‘rrelaxiv’
Namespaces in Imports field not imported from:
  ‘boot’ ‘splines’
  All declared Imports should be used.
Package suggested but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘devtools’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
Note: found 4 marked UTF-8 strings
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is  6.6Mb
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installed size is  9.5Mb
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'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘knitr’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.8Mb
  sub-directories of 1Mb or more:
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installed size is  5.2Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Rcplex’
installed size is  6.9Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.7Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ape’
  All declared Imports should be used.
installed size is  5.9Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'org.Dr.eg.db', 'scde'
installed size is  6.7Mb
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'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Note: found 4 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  8.3Mb
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Package which this enhances but not available for checking: ‘CorShrink’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘smoothmest’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
Package suggested but not available for checking: ‘Rmpi’
installed size is 16.2Mb
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'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘flexsurv’
  All declared Imports should be used.
installed size is  5.7Mb
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installed size is  7.2Mb
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'LazyData' is specified without a 'data' directory
installed size is 46.6Mb
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'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
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‘constparty.Rnw’... [3s/3s] OK
  ‘ctree.Rnw’ using ‘UTF-8’... [4s/4s] NOTE
differences from ‘ctree.Rout.save’
1409,1412d1408
< Deviance Residuals: 
<     Min       1Q   Median       3Q      Max  
< -45.801  -11.208   -1.049   10.903   53.615  
< 
  ‘mob.Rnw’... [5s/5s] OK
  ‘partykit.Rnw’... [1s/1s] OK
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘clusterProfiler’ ‘purrr’
  All declared Imports should be used.
installed size is  5.5Mb
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GNU make is a SystemRequirements.
Package required but not available: ‘Mfuzz’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 10.9Mb
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installed size is  6.7Mb
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installed size is  6.5Mb
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installed size is  6.8Mb
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installed size is  6.8Mb
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/pbdMPI.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘ade4’
  All declared Imports should be used.
Package required but not available: ‘pbdMPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
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installed size is  5.4Mb
  sub-directories of 1Mb or more:
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Malformed Description field: should contain one or more complete sentences.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 11.1Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 24.6Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘fda’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
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installed size is 133.1Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
installed size is 33.5Mb
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installed size is 34.0Mb
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'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'ggtreeExtra', 'Mfuzz'
Package suggested but not available for checking: ‘PythonInR’
installed size is 21.1Mb
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'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ncvreg’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘glmnet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 18.2Mb
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installed size is 134.4Mb
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GNU make is a SystemRequirements.
installed size is  6.4Mb
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Package suggested but not available for checking: ‘ptmixed’
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
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installed size is  9.2Mb
  sub-directories of 1Mb or more:
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installed size is 56.2Mb
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Package suggested but not available for checking: ‘DMwR’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘dendextendRcpp’
Namespace in Imports field not imported from: ‘rms’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.9Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 33.0Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
installed size is  7.9Mb
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'LazyData' is specified without a 'data' directory
Note: found 114 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
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installed size is  7.2Mb
  sub-directories of 1Mb or more:
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installed size is 44.7Mb
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Package required but not available: ‘LBE’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   3.5Mb
'LazyData' is specified without a 'data' directory
installed size is 62.8Mb
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Package suggested but not available for checking: ‘INLA’
installed size is 12.7Mb
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'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
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Namespace in Imports field not imported from: ‘FrF2.catlg128’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.4Mb
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Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘pipenostics-Ex.R’ failed
The error most likely occurred in:

> ### Name: mgtdhid
> ### Title: Get ground temperature
> ### Aliases: mgtdhid mgtdhidt mgtdhgeo mgtdhgeot
> 
> ### ** Examples
> 
>  # Let consider the next geographical positions:
>  lat <- c(s28434 = 56.65, s28418 = 56.47, s23711 = 62.70, ControlPoint = 57)
>  lon <- c(s28434 = 57.78, s28418 = 53.73, s23711 = 56.20, ControlPoint = 57)
>  
>  # * ground temperatures at first three locations on 02 March 2023 at depth 3 m:
>  mgtdhgeo(head(lat, 3), head(lon, 3), tau = as.POSIXct("2023-03-02"), depth = 3)
[1] 4.196030 4.779748 2.939201
> 
>  # * it is the same as obtaining ground temperatures from weather stations:
>  mgtdhid(id = c(28434L, 28418L, 23711L), tau = as.POSIXct("2023-03-02"), depth = 3)
[1] 4.196030 4.779748 2.939201
> 
>  # * undisturbed ground temperature plot at Control Point:
>  days <- as.POSIXct("2023-01-01") + 3600*24*(seq.int(1, 365) - 1)
>  plot(
+    days, 
+    mgtdhgeot(days, lat[["ControlPoint"]], lon[["ControlPoint"]]), 
+    type = "l", 
+    ylab = "Temperature, °C"
+  )
Error in mgtdhgeot(days, lat[["ControlPoint"]], lon[["ControlPoint"]]) : 
  Assertion on 'tau' failed: Element 1 is not >= 0.
Calls: plot ... xy.coords -> mgtdhgeot -> <Anonymous> -> makeAssertion -> mstop
Execution halted
installed size is 23.4Mb
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Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
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    data   2.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 22.8Mb
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installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘robustbase’
  All declared Imports should be used.
Package suggested but not available for checking: ‘slingshot’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘PlackettLuce’ ‘StatRank’ ‘pmr’ ‘prefmod’ ‘rankdist’
  All declared Imports should be used.
installed size is  5.7Mb
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installed size is 17.3Mb
  sub-directories of 1Mb or more:
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    libs  12.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mapproj’
  All declared Imports should be used.
Note: found 12992 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘hexbin’ ‘quantreg’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
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    htmlwidgets   4.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Package suggested but not available for checking: ‘Rmpi’
Package suggested but not available for checking: ‘Rmpi’
Namespace in Imports field not imported from: ‘ssh’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘base’ ‘grDevices’
  All declared Imports should be used.
Package suggested but not available for checking: ‘pmartRdata’
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Package required but not available: ‘pbdMPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Note: found 62 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
Namespaces in Imports field not imported from:
  ‘car’ ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 21 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘MASS’ ‘car’ ‘formula.tools’ ‘ggplot2’ ‘gplots’ ‘graphics’ ‘purrr’
  ‘rstatix’ ‘stringr’ ‘tidyverse’
  All declared Imports should be used.
Note: found 2 marked UTF-8 strings
Package suggested but not available for checking: ‘pollimetrydata’
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R         2.0Mb
    extdata   1.9Mb
'LazyData' is specified without a 'data' directory
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    R      7.1Mb
    data   4.6Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    1.8Mb
    libs   1.4Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    extdata   2.8Mb
    libs      2.9Mb
installed size is 19.5Mb
  sub-directories of 1Mb or more:
    libs  19.1Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data      2.7Mb
    extdata   3.5Mb
installed size is 42.2Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Package required but not available: ‘EmpiricalBrownsMethod’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is 38.7Mb
  sub-directories of 1Mb or more:
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installed size is 13.0Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc   6.2Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    doc  12.0Mb
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc  10.5Mb
Packages required and available but unsuitable versions:
  'graphics', 'grDevices', 'utils'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 11.5Mb
  sub-directories of 1Mb or more:
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    libs   8.5Mb
installed size is 13.4Mb
  sub-directories of 1Mb or more:
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    extdata  11.6Mb
Namespace in Imports field not imported from: ‘lazyeval’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    data   2.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 15.4Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.1Mb
  sub-directories of 1Mb or more:
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installed size is  5.5Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘tidyr’ ‘utils’
  All declared Imports should be used.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Packages suggested but not available for checking:
  'gurobi', 'Rcplex', 'rcbc'
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   5.7Mb
Packages suggested but not available for checking:
  'gurobi', 'rcbc', 'cplexAPI'
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    doc    4.7Mb
    libs  10.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 21.9Mb
  sub-directories of 1Mb or more:
    libs  21.6Mb
Namespaces in Imports field not imported from:
  ‘LaplacesDemon’ ‘epitools’ ‘rpivotTable’ ‘shiny’ ‘shinyMatrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc           8.8Mb
    htmlwidgets   2.5Mb
'LazyData' is specified without a 'data' directory
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    data   2.2Mb
    libs  12.9Mb
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
'LazyData' is specified without a 'data' directory
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    libs  17.5Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Package suggested but not available for checking: ‘cmdstanr’
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    libs  17.5Mb
installed size is 120.3Mb
  sub-directories of 1Mb or more:
    libs  119.9Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 35.7Mb
  sub-directories of 1Mb or more:
    libs  35.0Mb
Namespaces in Imports field not imported from:
  ‘StanHeaders’ ‘methods’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
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    libs   2.7Mb
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘grDevices’
  All declared Imports should be used.
installed size is 22.0Mb
  sub-directories of 1Mb or more:
    libs  21.9Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   3.1Mb
Note: found 12717 marked UTF-8 strings
Package suggested but not available for checking: ‘rdt’
Package suggested but not available for checking: ‘rdt’
Package suggested but not available for checking: ‘rdt’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rdt’
installed size is 26.4Mb
  sub-directories of 1Mb or more:
    libs  26.2Mb
Note: found 1 marked UTF-8 string
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
installed size is 127.4Mb
  sub-directories of 1Mb or more:
    libs  126.9Mb
GNU make is a SystemRequirements.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Package suggested but not available for checking: ‘cmdstanr’
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   3.0Mb
Namespaces in Imports field not imported from:
  ‘devtools’ ‘qpdf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
Note: found 26 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 28.2Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Note: found 107 marked UTF-8 strings
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
Package required but not available: ‘tweeDEseq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc        4.0Mb
    examples   2.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
installed size is 51.3Mb
  sub-directories of 1Mb or more:
    libs  50.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 31.6Mb
  sub-directories of 1Mb or more:
    libs  31.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is 16.5Mb
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Missing or unexported objects:
  ‘async::http_get’ ‘async::http_stop_for_status’ ‘async::synchronise’
  ‘async::when_all’
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘devtools’
  All declared Imports should be used.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
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    staticdocs   3.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R   5.1Mb
installed size is 79.8Mb
  sub-directories of 1Mb or more:
    libs  79.1Mb
'LazyData' is specified without a 'data' directory
installed size is 119.7Mb
  sub-directories of 1Mb or more:
    libs  118.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
Package suggested but not available for checking: ‘spDataLarge’
Namespaces in Imports field not imported from:
  ‘rmarkdown’ ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘missMethods’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.7Mb
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    libs  15.5Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
'LazyData' is specified without a 'data' directory
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    data  10.8Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    data  12.5Mb
Malformed Description field: should contain one or more complete sentences.
Note: found 6 marked UTF-8 strings
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  11.6Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    libs  16.4Mb
'LazyData' is specified without a 'data' directory
installed size is 38.0Mb
  sub-directories of 1Mb or more:
    extdata   3.3Mb
    libs     33.4Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    R         2.1Mb
    contrib   3.7Mb
    doc       3.0Mb
    libs      1.3Mb
Namespace in Imports field not imported from: ‘MatrixModels’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   8.0Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   3.1Mb
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> K_\text 
                   {max}
l.2230 ...to a user-specified \eqn{K_\text{max}}{}
                                                  )
! Undefined control sequence.
<argument> K_\text 
                   {max}
l.2256 ...er}{integer} scalar \eqn{K_\text{max}}{}
                                                  ,
! Undefined control sequence.
<argument> K^c+1=K_\text 
                         {max}
l.2282 ...is stopped if \eqn{K^c+1=K_\text{max}}{}
                                                  ,
Namespace in Imports field not imported from: ‘SparseM’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    lib    5.3Mb
    libs   5.6Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘fastshp’
Namespace in Imports field not imported from: ‘psych’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc         2.0Mb
    shiny_app   1.2Mb
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    libs  13.1Mb
Namespaces in Imports field not imported from:
  ‘pracma’ ‘zoo’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ReGenesees’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘data.table’ ‘dplyr’ ‘lmerTest’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘bootmlm’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    java   5.0Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    libs  19.2Mb
'library' or 'require' calls in package code:
  ‘RDCOMClient’ ‘rcom’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package suggested but not available for checking: ‘BRugs’
Package unavailable to check Rd xrefs: ‘BRugs’
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc   9.9Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc           5.3Mb
    htmlwidgets   1.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘asd’ ‘cubature’ ‘data.table’ ‘ggplot2’ ‘multxpert’ ‘survival’
  All declared Imports should be used.
Package suggested but not available for checking: ‘slingshot’
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    6.7Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
installed size is 25.1Mb
  sub-directories of 1Mb or more:
    doc           5.3Mb
    htmlwidgets   1.8Mb
    libs         16.0Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘car’ ‘dplyr’ ‘grid’ ‘gridExtra’ ‘knitr’ ‘lmerTest’ ‘tidyr’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data      2.2Mb
    extdata   1.4Mb
Namespace in Imports field not imported from: ‘gridExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 42.5Mb
  sub-directories of 1Mb or more:
    libs  42.3Mb
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘ragtop_convertibles_in_r.Rmd’ using rmarkdown
Quitting from lines 425-461 (ragtop_convertibles_in_r.Rmd) 
Error: processing vignette 'ragtop_convertibles_in_r.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘ragtop_convertibles_in_r.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 34.7Mb
  sub-directories of 1Mb or more:
    libs  33.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    htmlwidgets       10.0Mb
    super-tiny-icons   1.0Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    api           3.1Mb
    htmlwidgets   7.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Spectra’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘curl’ ‘jsonlite’
  All declared Imports should be used.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    doc       1.7Mb
    extdata   4.1Mb
    libs      9.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    libs   6.6Mb
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is 66.2Mb
  sub-directories of 1Mb or more:
    libs  65.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    libs  13.0Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'cairoDevice', 'RGtk2'
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
    etc    1.9Mb
    po     1.2Mb
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    libs  11.3Mb
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘withr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 21.6Mb
  sub-directories of 1Mb or more:
    libs  20.9Mb
Package suggested but not available for checking: ‘raybevel’
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    libs   3.3Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
Namespace in Imports field not imported from: ‘rex’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   1.1Mb
    libs      3.7Mb
GNU make is a SystemRequirements.
installed size is 57.1Mb
  sub-directories of 1Mb or more:
    libs  55.1Mb
GNU make is a SystemRequirements.
installed size is 58.2Mb
  sub-directories of 1Mb or more:
    libs  57.6Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rhdf5’
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/Rblpapi.Rcheck/00install.out’ for details.
installed size is 44.1Mb
  sub-directories of 1Mb or more:
    libs  42.9Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    libs  13.8Mb
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 26334 marked UTF-8 strings
Package suggested but not available for checking: ‘rrelaxiv’
'LazyData' is specified without a 'data' directory
installed size is 66.1Mb
  sub-directories of 1Mb or more:
    libs  65.4Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’ ‘shinythemes’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rrelaxiv’
'LazyData' is specified without a 'data' directory
installed size is 20.2Mb
  sub-directories of 1Mb or more:
    cont  20.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    libs  13.0Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rqubic’

Depends: includes the non-default packages:
  'biclust', 'fabia', 'iBBiG', 'superbiclust', 'BcDiag', 'BicARE',
  's4vd', 'BiBitR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ROpenOffice’
Depends: includes the non-default packages:
  'IQCC', 'qcc', 'qicharts2', 'randtests', 'rmarkdown',
  'TeachingDemos', 'tseries'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   3.5Mb
    po    2.4Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    corpora   7.5Mb
Packages suggested but not available for checking: 'ROntoTools', 'oligo'
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/Rcplex.Rcheck/00install.out’ for details.
installed size is 19.9Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  17.7Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    include   6.5Mb
    libs      2.1Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
installed size is 45.7Mb
  sub-directories of 1Mb or more:
    include  45.6Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 34.0Mb
  sub-directories of 1Mb or more:
    include   9.5Mb
    libs     24.0Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/RcppMeCab.Rcheck/00install.out’ for details.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    include   6.7Mb
    libs      2.5Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
GNU make is a SystemRequirements.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    include   6.3Mb
    libs      4.9Mb
installed size is 17.8Mb
  sub-directories of 1Mb or more:
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    jsonexamples   3.8Mb
    libs          11.7Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    include   1.1Mb
    libs      5.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 20.4Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs  16.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘gtools’
  All declared Imports should be used.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    R      4.6Mb
    data   1.5Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
Package suggested but not available for checking: ‘dataui’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Running examples in ‘realTimeloads-Ex.R’ failed
The error most likely occurred in:

> ### Name: impute_data
> ### Title: Returns x with gaps imputed using ARIMA and Decision Trees,
> ###   optional uncertainty estimation using Monte Carlo resampling
> ### Aliases: impute_data
> 
> ### ** Examples
> 
> # Impute non-tidal data
> time <- realTimeloads::ExampleData$Sediment_Samples$time
> xo <- realTimeloads::ExampleData$Sediment_Samples$SSCxs_mg_per_liter
> Q <- realTimeloads::ExampleData$Discharge$Discharge_m_cubed_per_s
> idata <- sample(1:length(xo),round(length(xo)*0.5),replace=FALSE)
> x <- rep(NA,length(xo))
> x[idata] <- xo[idata] # simulated samples
> flow_concentrtion_ratio <- imputeTS::na_interpolation(Q/x)
> Xreg <- cbind(Q,flow_concentrtion_ratio)
> Output <- impute_data(time,x,Xreg,MC = 10,ptrain = 0.8)
Error in optim(init[mask], getLike, method = "L-BFGS-B", lower = rep(0,  : 
  L-BFGS-B needs finite values of 'fn'
Calls: impute_data -> <Anonymous> -> <Anonymous> -> optim
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   1.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required and available but unsuitable version: ‘stats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   2.5Mb
'LazyData' is specified without a 'data' directory
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    htmlwidgets   9.8Mb
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   9.0Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   3.1Mb
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Package suggested but not available for checking: ‘Rmpi’
installed size is 18.4Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs  14.5Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
Namespaces in Imports field not imported from:
  ‘SemiPar’ ‘caret’ ‘dplyr’ ‘scales’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 2 marked Latin-1 strings
  Note: found 50022 marked UTF-8 strings
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   4.7Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    include   6.3Mb
    libs      4.6Mb
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Rmpi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘Rcplex’
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    libs   3.8Mb
'LazyData' is specified without a 'data' directory
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    libs  16.6Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   5.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   9.9Mb
Packages suggested but not available for checking: 'PADOG', 'safe'
Packages unavailable to check Rd xrefs: ‘PADOG’, ‘safe’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   6.8Mb
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs  13.5Mb
GNU make is a SystemRequirements.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   1.3Mb
    java      2.9Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs      3.3Mb
    swagger   1.4Mb
installed size is 23.1Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    libs     19.5Mb
    models    1.6Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
Package suggested but not available for checking: ‘ccdata’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    examples   1.9Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘BSgenome.Hsapiens.UCSC.hg38’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required and available but unsuitable version: ‘ggtree’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RevGadgets’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 22.0Mb
  sub-directories of 1Mb or more:
    libs  21.2Mb
installed size is 44.6Mb
  sub-directories of 1Mb or more:
    libs  43.2Mb
Namespace in Imports field not imported from: ‘sf’
  All declared Imports should be used.
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    data  14.1Mb
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Namespace in Imports field not imported from: ‘titanic’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data      1.9Mb
    doc       1.2Mb
    extdata   1.9Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 27.9Mb
  sub-directories of 1Mb or more:
    libs  26.7Mb
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
Warning in py_initialize(config$python, config$libpython, config$pythonhome,  :
  Python 2 reached EOL on January 1, 2020. Python 2 compatability be removed in an upcoming reticulate release.

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
installed size is 29.7Mb
  sub-directories of 1Mb or more:
    doc     3.0Mb
    fonts   1.5Mb
    libs   22.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    doc          10.3Mb
    htmlwidgets   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'mimic.demo', 'eicu.demo'
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs  15.2Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘RInside/libs/RInside.so’:
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘RInside.o’
File ‘RInside/libs/RInside.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CleanTempDir’,
    ‘R_DefParams’, ‘R_ReplDLLinit’, ‘R_RunExitFinalizers’,
    ‘R_SetParams’, ‘R_SignalHandlers’, ‘R_TempDir’, ‘Rf_endEmbeddedR’,
    ‘Rf_initEmbeddedR’, ‘run_Rmainloop’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    libs  13.0Mb
'LazyData' is specified without a 'data' directory
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  22.4Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   8.7Mb
Namespace in Imports field not imported from: ‘httr’
  All declared Imports should be used.
Note: found 243 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/rJava.Rcheck/00install.out’ for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    java   4.2Mb
Namespace in Imports field not imported from: ‘coda’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 55.9Mb
  sub-directories of 1Mb or more:
    include   3.4Mb
    libs     51.6Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.0Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.8Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    datasets  10.2Mb
installed size is 28.3Mb
  sub-directories of 1Mb or more:
    R     4.0Mb
    exe  23.8Mb
'LazyData' is specified without a 'data' directory
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    libs  19.7Mb
installed size is 24.7Mb
  sub-directories of 1Mb or more:
    extdata  24.0Mb
'LazyData' is specified without a 'data' directory
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
installed size is 19.4Mb
  sub-directories of 1Mb or more:
    lemon   2.8Mb
    libs   16.4Mb
'LazyData' is specified without a 'data' directory
installed size is 103.5Mb
  sub-directories of 1Mb or more:
    libs  102.7Mb
GNU make is a SystemRequirements.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/rlibkriging.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'DoubletFinder', 'EnhancedVolcano', 'RcppPlanc'
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
'LazyData' is specified without a 'data' directory
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    rmd   6.0Mb
Found the following significant warnings:
  Warning: Software mark not found in path.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/RMark.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
installed size is 132.0Mb
  sub-directories of 1Mb or more:
    libs  131.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/RmecabKo.Rcheck/00install.out’ for details.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> ... (t+(r-1))\neq \mu (t+(s-1))\ \text 
                                                  {for some}\ t\in [0,1],\\ ...
l.380 \end{array}\right.}{}
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    libs   5.7Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs       1.2Mb
    minizinc   3.3Mb
'LazyData' is specified without a 'data' directory
installed size is 38.9Mb
  sub-directories of 1Mb or more:
    libs  38.0Mb
installed size is 27.5Mb
  sub-directories of 1Mb or more:
    libs  27.3Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/Rmpi.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
installed size is 84.3Mb
  sub-directories of 1Mb or more:
    libs  83.7Mb
Package unavailable to check Rd xrefs: ‘cmdstanr’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘quadprog’
  All declared Imports should be used.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
GNU make is a SystemRequirements.
installed size is 18.9Mb
  sub-directories of 1Mb or more:
    libs  17.6Mb
Package required but not available: ‘R4RNA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 19.7Mb
  sub-directories of 1Mb or more:
    libs  19.5Mb
Package suggested but not available for checking: ‘recount3’
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    doc    2.2Mb
Package suggested but not available for checking: ‘rnaturalearthhires’
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.1Mb
Malformed Title field: should not end in a period.
installed size is 20.6Mb
  sub-directories of 1Mb or more:
    libs  20.4Mb
Namespace in Imports field not imported from: ‘qtl’
  All declared Imports should be used.
Packages which this enhances but not available for checking:
  'pbdMPI', 'Rmpi'
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Packages unavailable to check Rd xrefs: ‘pbdMPI’, ‘Rmpi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 101.0Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs     98.8Mb
'LazyData' is specified without a 'data' directory
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    libs  12.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    doc    1.7Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    R  11.4Mb
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs  15.3Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
Namespace in Imports field not imported from: ‘memoise’
  All declared Imports should be used.
installed size is 22.0Mb
  sub-directories of 1Mb or more:
    libs  21.8Mb
Package suggested but not available for checking: ‘illuminaHumanv3.db’
Namespace in Imports field not imported from: ‘glmnet’
  All declared Imports should be used.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Namespace in Imports field not imported from: ‘future’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is 95.7Mb
  sub-directories of 1Mb or more:
    libs  94.9Mb
GNU make is a SystemRequirements.
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    libs  17.2Mb
installed size is 26.6Mb
  sub-directories of 1Mb or more:
    libs  26.0Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   4.9Mb
'LazyData' is specified without a 'data' directory
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc               1.7Mb
    libs              5.0Mb
    simulationStudy   1.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘progress’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Rcplex’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    doc  15.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
GNU make is a SystemRequirements.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R         3.0Mb
    extdata   2.7Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
sh: cmake: command not found
sh: cmake: command not found
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
sh: cmake: command not found
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
sh: cmake: command not found
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
sh: cmake: command not found
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
sh: cmake: command not found
sh: cmake: command not found
sh: cmake: command not found
sh: cmake: command not found
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/ROracle.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   2.7Mb
    libs   5.4Mb
Namespace in Imports field not imported from: ‘geometry’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    R      5.0Mb
    libs   7.7Mb
installed size is 59.5Mb
  sub-directories of 1Mb or more:
    libs  58.3Mb
GNU make is a SystemRequirements.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is 20.6Mb
  sub-directories of 1Mb or more:
    libs  19.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   6.3Mb
'LazyData' is specified without a 'data' directory
installed size is 47.6Mb
  sub-directories of 1Mb or more:
    libs  47.5Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   5.7Mb
'LazyData' is specified without a 'data' directory
installed size is 33.3Mb
  sub-directories of 1Mb or more:
    libs  32.0Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  /opt/R/arm64/include/boost/math/tools/config.hpp:23:6: warning: "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-W#warnings]
  #    warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/RQuantLib.Rcheck/00install.out’ for details.
installed size is 103.3Mb
  sub-directories of 1Mb or more:
    libs  102.7Mb
Namespace in Imports field not imported from: ‘NatureSounds’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   3.6Mb
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘abind’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
Namespaces in Imports field not imported from:
  ‘keys’ ‘shinyWidgets’ ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
GNU make is a SystemRequirements.
Note: information on .o files is not available
File ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/Rserve.Rcheck/Rserve/libs/Rserve.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_exit’, possibly from ‘exit’ (C)
  Found ‘_rand’, possibly from ‘rand’ (C)
  Found ‘_random’, possibly from ‘random’ (C)
  Found ‘_srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API calls to R: ‘R_Consolefile’, ‘R_InputHandlers’,
    ‘R_Outputfile’, ‘R_TempDir’, ‘R_Visible’, ‘addInputHandler’,
    ‘ptr_R_Busy’, ‘ptr_R_ClearerrConsole’, ‘ptr_R_FlushConsole’,
    ‘ptr_R_ReadConsole’, ‘ptr_R_ResetConsole’, ‘ptr_R_ShowMessage’,
    ‘ptr_R_WriteConsole’, ‘ptr_R_WriteConsoleEx’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 26.0Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs  24.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Namespace in Imports field not imported from: ‘h2o’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
Namespace in Imports field not imported from: ‘MatrixExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is 44.9Mb
  sub-directories of 1Mb or more:
    libs  44.3Mb
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    libs  11.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 296.7Mb
  sub-directories of 1Mb or more:
    R       2.0Mb
    doc     4.7Mb
    libs  289.2Mb
GNU make is a SystemRequirements.
installed size is 67.1Mb
  sub-directories of 1Mb or more:
    libs  66.8Mb
GNU make is a SystemRequirements.
installed size is 36.6Mb
  sub-directories of 1Mb or more:
    libs  36.0Mb
GNU make is a SystemRequirements.
installed size is 49.0Mb
  sub-directories of 1Mb or more:
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    libs  11.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
installed size is 36.5Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘mc2d’
  All declared Imports should be used.
installed size is 29.0Mb
  sub-directories of 1Mb or more:
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installed size is 23.4Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
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Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
Namespaces in Imports field not imported from:
  ‘httr’ ‘logger’
  All declared Imports should be used.
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    rmarkdown  11.1Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
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installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is 99.8Mb
  sub-directories of 1Mb or more:
    libs  98.1Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R   6.0Mb
Running examples in ‘rtrend-Ex.R’ failed
The error most likely occurred in:

> ### Name: slope_rast
> ### Title: calculate slope of rast object
> ### Aliases: slope_rast rast_filter_time
> 
> ### ** Examples
> 
> library(rtrend)
> library(terra)
terra 1.7.71
> 
> f <- system.file("rast/MOD15A2_LAI_China_G050_2001-2020.tif", package = "rtrend")
> r <- rast(f)
> r
class       : SpatRaster 
dimensions  : 80, 140, 20  (nrow, ncol, nlyr)
resolution  : 0.5, 0.5  (x, y)
extent      : 70, 140, 15, 55  (xmin, xmax, ymin, ymax)
coord. ref. : lon/lat WGS 84 (EPSG:4326) 
source      : MOD15A2_LAI_China_G050_2001-2020.tif 
names       :      LAI,      LAI,      LAI,     LAI,      LAI,      LAI, ... 
min values  : 0.000000, 0.000000, 0.000000, 0.00000, 0.000000, 0.000000, ... 
max values  : 5.692542, 5.479348, 5.585326, 5.33587, 5.822826, 5.533152, ... 
time        : 978307200 to 1577836800 
> time(r)
 [1]  978307200 1009843200 1041379200 1072915200 1104537600 1136073600
 [7] 1167609600 1199145600 1230768000 1262304000 1293840000 1325376000
[13] 1356998400 1388534400 1420070400 1451606400 1483228800 1514764800
[19] 1546300800 1577836800
> 
> slp <- slope_rast(r,
+   period = c(2001, 2020), 
+   outfile = "LAI_trend.tif", overwrite = TRUE,
+   fun = rtrend::slope_mk, .progress = "none"
+ )
Error in as.POSIXlt.numeric(x, tz = tz(x)) : 'origin' must be supplied
Calls: slope_rast ... year -> year.default -> as.POSIXlt -> as.POSIXlt.numeric
Execution halted
Running ‘testthat.R’ [3s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── Error ('test-slope_rast.R:9:3'): slope_rast works ───────────────────────────
  Error in `as.POSIXlt.numeric(x, tz = tz(x))`: 'origin' must be supplied
  Backtrace:
      ▆
   1. ├─rtrend::slope_rast(...) at test-slope_rast.R:9:3
   2. │ └─r %<>% rast_filter_time(period)
   3. └─rtrend::rast_filter_time(., period)
   4.   ├─lubridate::year(time(r))
   5.   └─lubridate:::year.default(time(r))
   6.     ├─base::as.POSIXlt(x, tz = tz(x))
   7.     └─base::as.POSIXlt.numeric(x, tz = tz(x))
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 23 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘slope_rast.Rmd’ using rmarkdown

Quitting from lines 20-33 [setup] (slope_rast.Rmd)
Error: processing vignette 'slope_rast.Rmd' failed with diagnostics:
'origin' must be supplied
--- failed re-building ‘slope_rast.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
installed size is 28.6Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs  19.9Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘cmdstanr’
installed size is 216.3Mb
  sub-directories of 1Mb or more:
    data    1.5Mb
    libs  213.9Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    libs   2.5Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   6.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Non-standard license specification:
  CECILL-2.1
Standardizable: FALSE
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘glmmADMB’
Package required but not available: ‘rWikiPathways’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 45.1Mb
  sub-directories of 1Mb or more:
    libs  43.9Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gpuR’
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    include   5.1Mb
installed size is 63.3Mb
  sub-directories of 1Mb or more:
    include   5.0Mb
    libs     57.9Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rWCVPdata’
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data      3.0Mb
    extdata   2.4Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
'LazyData' is specified without a 'data' directory
Note: found 4250 marked UTF-8 strings
Note: found 6 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
Packages suggested but not available for checking:
  'BiocPkgTools', 'biocViews'
Packages unavailable to check Rd xrefs: ‘BiocPkgTools’, ‘biocViews’
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    3.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    libs  16.6Mb
installed size is 32.5Mb
  sub-directories of 1Mb or more:
    libs  32.2Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs    8.1Mb
    yacas   1.3Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs    8.8Mb
    yacas   1.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    libs  16.0Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
installed size is 36.5Mb
  sub-directories of 1Mb or more:
    libs  35.4Mb
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    libs  16.9Mb
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    libs  15.5Mb
'LazyData' is specified without a 'data' directory
installed size is 22.3Mb
  sub-directories of 1Mb or more:
    libs  22.1Mb
installed size is 46.9Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs  44.3Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.4Mb
    libs   4.0Mb
Packages suggested but not available for checking:
  'GO.db', 'GOstats', 'org.Sc.sgd.db'
Note: found 6 marked UTF-8 strings
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 46.8Mb
  sub-directories of 1Mb or more:
    libs  46.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Package required and available but unsuitable version: ‘pcaMethods’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [51s/56s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-armacalc.R:60:1'): functions in armacalc.R work ok ─────────────
  Error in `InformationMatrixARMA(phi22, -theta22)`: could not find function "InformationMatrixARMA"
  Backtrace:
      ▆
   1. └─testthat::expect_equal(...) at test-armacalc.R:60:1
   2.   └─testthat::quasi_label(enquo(expected), expected.label, arg = "expected")
   3.     └─rlang::eval_bare(expr, quo_get_env(quo))
  ── Error ('test-armacalc.R:117:5'): ARMA information matrix in armacalc.R is ok ──
  Error in `InformationMatrixARMA(-c(-0.8, 0.1), -0.5)`: could not find function "InformationMatrixARMA"
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 217 ]
  Error: Test failures
  Execution halted
Namespaces in Imports field not imported from:
  ‘httr’ ‘jsonlite’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    bin   4.4Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.3Mb
GNU make is a SystemRequirements.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc       5.1Mb
    extdata   1.2Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
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LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<recently read> \dfrac 
                       
l.192 ...omputed by  \eqn{\dfrac{|I|-ec}{|I|-1}}{}
                                                  .
! Undefined control sequence.
<argument> 1 - \dfrac 
                      {\hat {\ell }_{k,n}(1_I,0_{I^c})}{|I|}
l.280 ...ac{\hat{\ell}_{k,n}(1_I,0_{I^c})}{|I|}}{}
                                                  .
! Undefined control sequence.
<argument> S_I(\ell )=\dfrac 
                             {D_I(\ell )}{D(\ell )}
l.1278 ...{S_I(\ell)=\dfrac{D_I(\ell)}{D(\ell)}}{}
                                                  .
! Undefined control sequence.
<argument> S_I(\ell )=\dfrac 
                             {D_I(\ell )}{D(\ell )}
l.1364 ...{S_I(\ell)=\dfrac{D_I(\ell)}{D(\ell)}}{}
                                                  .
! Undefined control sequence.
<argument> \hat {S}_{I,k,n}=\dfrac 
                                   {\hat {D}_{I,k,n}}{\hat {D}_{k,n}}
l.1374 ...dfrac{\hat{D}_{I,k,n}}{\hat{D}_{k,n}}}{}
                                                  
! Undefined control sequence.
<recently read> \dfrac 
                       
l.1607 ...hat{\Upsilon}_{I,k,n}}{\hat{D}_{k,n}}}{}
                                                   the empirical counterpart...
! Undefined control sequence.
<recently read> \dfrac 
                       
l.1607 ...n{\dfrac{\Upsilon_I(\ell)}{D_I(\ell)}}{}
                                                  .
! Undefined control sequence.
<recently read> \dfrac 
                       
l.1609 ... by \eqn{\dfrac{(2|I|+2)!}{2(|I|!)^2}}{}
                                                  .
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘crayon’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
Namespace in Imports field not imported from: ‘network’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   3.6Mb
'LazyData' is specified without a 'data' directory
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex', 'pogs'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘cowplot’ ‘ggplot2’ ‘ggridges’ ‘ggstance’ ‘jmvcore’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Packages suggested but not available for checking:
  'DropletUtils', 'Nebulosa'
Packages unavailable to check Rd xrefs: ‘DropletUtils’, ‘Nebulosa’
Package required but not available: ‘glmGamPoi’

Packages suggested but not available for checking: 'scran', 'Linnorm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    libs   2.9Mb
Packages suggested but not available for checking: 'ontoProc', 'rrvgo'
'LazyData' is specified without a 'data' directory
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    libs  16.3Mb
Namespaces in Imports field not imported from:
  ‘devtools’ ‘mathjaxr’
  All declared Imports should be used.
Package required but not available: ‘LoomExperiment’

Packages suggested but not available for checking:
  'scRNAseq', 'sceasy', 'SeuratDisk', 'SeuratWrappers',
  'zellkonverter', 'GEOfastq'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required and available but unsuitable version: ‘UCell’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘scran’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘pracma’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RhpcBLASctl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'AUCell', 'decoupleR', 'infercnv', 'Nebulosa'
Package unavailable to check Rd xrefs: ‘infercnv’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘oligoClasses’
Namespaces in Imports field not imported from:
  ‘BiocManager’ ‘crayon’ ‘knitr’ ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘methods’ ‘pbapply’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘glmGamPoi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Note: found 2 marked UTF-8 strings
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   5.2Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
installed size is 87.7Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R   8.0Mb
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    extdata  18.0Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs  14.5Mb
GNU make is a SystemRequirements.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    libs   7.7Mb
Packages required but not available: 'ggmsa', 'msa'

Package suggested but not available for checking: ‘org.Rn.eg.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rsbml’
Package suggested but not available for checking: ‘ArrayExpress’
Package unavailable to check Rd xrefs: ‘ArrayExpress’
Found the following apparent S3 methods exported but not registered:
  vcov.stepmented
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘flowMerge’
Package unavailable to check Rd xrefs: ‘flowMerge’
Error(s) in re-building vignettes:
  ...
--- re-building ‘SEI_vignette.Rnw’ using knitr
Error: processing vignette 'SEI_vignette.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'SEI_vignette.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm8): Font bbm8 at 600 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘SEI_vignette.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘cluster’ ‘factoextra’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘FD’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 34.5Mb
  sub-directories of 1Mb or more:
    www  34.4Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘lavaan’ ‘psych’ ‘semPlot’ ‘semTools’ ‘shinyAce’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’ ‘webp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘editData’ ‘miniUI’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘reticulate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      2.2Mb
    libs   2.4Mb
installed size is 23.1Mb
  sub-directories of 1Mb or more:
    libs    21.4Mb
    models   1.6Mb
Note: found 836 marked UTF-8 strings
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.3Mb
Note: found 4436 marked UTF-8 strings
GNU make is a SystemRequirements.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   4.2Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
'LazyData' is specified without a 'data' directory
Package required but not available: ‘widgetTools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    doc    6.4Mb
    libs  10.3Mb
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    libs  17.8Mb
GNU make is a SystemRequirements.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
    libs   1.2Mb
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   4.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    libs  15.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘BPCells’
Packages suggested but not available for checking:
  'BPCells', 'monocle', 'presto'
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   8.2Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   4.9Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
installed size is 261.5Mb
  sub-directories of 1Mb or more:
    doc       1.7Mb
    libs    255.1Mb
    sqlite    1.5Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘plyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   7.5Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   1.0Mb
    doc    3.8Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘kableExtra’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rCOSA’
Package unavailable to check Rd xrefs: ‘rCOSA’
Package suggested but not available for checking: ‘hydromad’
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc       1.7Mb
    extdata   4.2Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/shide.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    www   7.7Mb
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Package suggested but not available for checking: ‘cmdstanr’
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    www   9.4Mb
'LazyData' is specified without a 'data' directory
installed size is 20.5Mb
  sub-directories of 1Mb or more:
    www  19.7Mb
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    www   7.6Mb
Namespace in Imports field not imported from: ‘reactable’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘httr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘KGode’ ‘XML’ ‘ggplot2’ ‘gridExtra’ ‘mvtnorm’ ‘reshape2’ ‘shinyjs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘scales’ ‘websocket’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    shinyApp  21.0Mb
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘shiny’ ‘shinyjs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    www  10.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘e1071’ ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument> X \in \mathbb 
                         {R}{n\times p}
l.3264 ...data \eqn{X \in \mathbb{R}{n\times p}}{}
                                                   such that its rows are
! Undefined control sequence.
<argument> ...Delta _{p-1} =\lbrace z \in \mathbb 
                                                  {R}^p~|~z_j > 0, \sum _{i=...
l.3267 }{}
           test whether the data is uniformly distributed.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1231 marked UTF-8 strings
Note: found 28 marked UTF-8 strings
Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg19’
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    help      1.7Mb
Packages suggested but not available for checking:
  'chromVAR', 'TFBSTools', 'motifmatchr'
Packages unavailable to check Rd xrefs: ‘motifmatchr’, ‘TFBSTools’, ‘chromVAR’
Package suggested but not available for checking: ‘rhdf5’
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘grid’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘doMPI’
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc   6.5Mb
Namespaces in Imports field not imported from:
  ‘pedtools’ ‘readr’
  All declared Imports should be used.
installed size is 18.6Mb
  sub-directories of 1Mb or more:
    extdata  13.0Mb
    libs      4.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs   2.7Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
GNU make is a SystemRequirements.
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs  12.6Mb
Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg38’
Note: found 1 marked UTF-8 string
Namespace in Imports field not imported from: ‘DBI’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.5Mb
Package suggested but not available for checking: ‘Rmpi’
Package unavailable to check Rd xrefs: ‘Rmpi’
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘metafor’
  All declared Imports should be used.
installed size is 22.3Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  19.9Mb
Namespaces in Imports field not imported from:
  ‘crqa’ ‘plot3D’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.7Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magrittr’ ‘psych’ ‘stringr’
  All declared Imports should be used.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    libs   6.8Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
Packages suggested but not available for checking: 'graph', 'Rgraphviz'
Packages unavailable to check Rd xrefs: ‘Rgraphviz’, ‘graph’
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘data.table’ ‘dplyr’ ‘lubridate’ ‘rmarkdown’ ‘yaml’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    R         2.0Mb
    extdata   1.6Mb
    libs      5.0Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘methods’
  All declared Imports should be used.
Note: found 2 marked UTF-8 strings
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
Package which this enhances but not available for checking: ‘kmndirs’
Unavailable namespace imported from by a ':::' call: ‘kmndirs’
  See the note in ?`:::` about the use of this operator.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   5.0Mb
GNU make is a SystemRequirements.
installed size is 38.2Mb
  sub-directories of 1Mb or more:
    libs  37.6Mb
Namespace in Imports field not imported from: ‘maps’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘numDeriv’ ‘png’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘RcppArmadillo’
  All declared Imports should be used.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
Note: found 23 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 20.7Mb
  sub-directories of 1Mb or more:
    libs  20.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
Namespaces in Imports field not imported from:
  ‘checkmate’ ‘glmnet’ ‘mice’
  All declared Imports should be used.
Note: found 2 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
GNU make is a SystemRequirements.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘covr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘SMITIDstruct’
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Namespaces in Imports field not imported from:
  ‘compiler’ ‘lmtest’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    3.3Mb
    libs  10.3Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘ggplot2’
  All declared Imports should be used.
Package suggested but not available for checking: ‘Rmpi’
Package suggested but not available for checking: ‘Rmpi’
Package which this enhances but not available for checking: ‘Rmpi’
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    extdata   3.1Mb
    libs      2.9Mb
Package required but not available: ‘GWASTools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘FactoMineR’ ‘flextable’ ‘htmlTable’ ‘stringr’
  All declared Imports should be used.
Note: found 938 marked UTF-8 strings
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘lgr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data      3.8Mb
    extdata   1.1Mb
Namespace in Imports field not imported from: ‘rlist’
  All declared Imports should be used.
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    doc    1.3Mb
    libs   9.6Mb
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [18s/31s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  `expected`: "0427" "1946"
  ── Failure ('test-audioblastProcessors.R:103:3'): .calcTimesOfDay() works as expected ──
  as.character(o[2, ]) (`actual`) not equal to c("2248", "0124") (`expected`).
  
  `actual`:   "2254" "0119"
  `expected`: "2248" "0124"
  ── Failure ('test-audioblastProcessors.R:105:3'): .calcTimesOfDay() works as expected ──
  as.character(o[4, ]) (`actual`) not equal to c("1206", "2248") (`expected`).
  
  `actual`:   "1207" "2254"
  `expected`: "1206" "2248"
  
  [ FAIL 18 | WARN 0 | SKIP 7 | PASS 811 ]
  Error: Test failures
  Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RSQLite’ ‘dbplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘SciencesPo’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘DropletUtils’
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
    doc    1.0Mb
Package suggested but not available for checking: ‘gridlayout’
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs  13.0Mb
Namespace in Imports field not imported from: ‘RcppEigen’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   2.3Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    include   2.1Mb
    libs      3.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   2.6Mb
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R   4.9Mb
'LazyData' is specified without a 'data' directory
installed size is 38.1Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    libs  33.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    java   1.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘gtable’ ‘rlang’ ‘testthat’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    libs  16.5Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘future’ ‘geosphere’ ‘lubridate’ ‘tidyverse’ ‘viridis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 35.2Mb
  sub-directories of 1Mb or more:
    libs  34.5Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘irlba’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/spaths.Rcheck/00install.out’ for details.
Packages required but not available:
  'SpatialExperiment', 'zinbwave', 'scran'

Package suggested but not available for checking: ‘bluster’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘INLA’
installed size is 54.6Mb
  sub-directories of 1Mb or more:
    libs  53.5Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    help   1.7Mb
    libs   1.2Mb
installed size is 13.0Mb
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GNU make is a SystemRequirements.
installed size is  6.0Mb
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GNU make is a SystemRequirements.
installed size is  5.1Mb
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Depends: includes the non-default packages:
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Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
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Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.sparse', 'spatstat.geom',
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Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.geom', 'spatstat.random',
  'spatstat.explore', 'nlme', 'rpart'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.geom', 'spatstat.random',
  'spatstat.explore', 'spatstat.model', 'spatstat.linnet'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
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installed size is 22.5Mb
  sub-directories of 1Mb or more:
    libs  21.6Mb
installed size is 13.6Mb
  sub-directories of 1Mb or more:
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    libs  10.1Mb
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
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Package suggested but not available for checking: ‘spDataLarge’
installed size is  6.6Mb
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installed size is  5.9Mb
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Note: found 34 marked UTF-8 strings
installed size is  8.2Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
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installed size is  6.0Mb
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Undocumented S4 methods:
  generic '[' and siglist 'SpectraInTime,ANY,missing,ANY'
  generic '[' and siglist 'SpectraInTime,missing,ANY,ANY'
  generic '[' and siglist 'SpectraInTime,missing,missing,ANY'
  generic '[' and siglist 'SpectraInTimeComp,ANY,ANY,ANY'
  generic '[' and siglist 'SpectraInTimeComp,ANY,missing,ANY'
  generic '[' and siglist 'SpectraInTimeComp,missing,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
installed size is  7.4Mb
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'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
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Namespaces in Imports field not imported from:
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'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
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installed size is 22.2Mb
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'LazyData' is specified without a 'data' directory
installed size is  8.4Mb
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Namespaces in Imports field not imported from:
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installed size is 17.2Mb
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installed size is  6.6Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
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Namespace in Imports field not imported from: ‘biomod2’
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installed size is 16.3Mb
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installed size is  6.1Mb
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'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [5s/7s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    1. ├─... %>% as_preview() at test-spork.R:297:1
    2. ├─spork::as_preview(.)
    3. └─spork:::as_preview.plotmath(.)
    4.   ├─latexpdf::as.png(...)
    5.   └─spork:::as.png.plotmath(...)
    6.     ├─ggplot2::ggplot(x, ...)
    7.     └─spork:::ggplot.plotmath(x, ...)
    8.       ├─ggplot2::ggplot(data.frame(x = 1, y = 1, label = (x)))
    9.       └─base::data.frame(x = 1, y = 1, label = (x))
   10.         ├─base::as.data.frame(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors)
   11.         └─base::as.data.frame.default(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors)
  
  [ FAIL 1 | WARN 0 | SKIP 7 | PASS 102 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
Note: found 199 marked UTF-8 strings
installed size is  7.1Mb
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installed size is 51.3Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
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installed size is 13.3Mb
  sub-directories of 1Mb or more:
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installed size is  8.7Mb
  sub-directories of 1Mb or more:
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installed size is  5.6Mb
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 35 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 28.1Mb
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'LazyData' is specified without a 'data' directory
installed size is 104.3Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘scanstatistics’
Namespace in Imports field not imported from: ‘e1071’
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is 28.7Mb
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is 48.8Mb
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installed size is 17.0Mb
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GNU make is a SystemRequirements.
installed size is 90.0Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘starsdata’
installed size is  6.4Mb
  sub-directories of 1Mb or more:
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Note: found 14 marked UTF-8 strings
Namespaces in Imports field not imported from:
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  ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘asreml’
Package suggested but not available for checking: ‘asreml’
installed size is  5.0Mb
  sub-directories of 1Mb or more:
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installed size is  7.2Mb
  sub-directories of 1Mb or more:
    extdata   2.4Mb
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installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
Package suggested but not available for checking: ‘asreml’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following possibly unsafe calls:
File ‘statnet.common/R/control.utilities.R’:
  unlockBinding("snctrl", environment(snctrl))
  unlockBinding("snctrl", environment(update_my_snctrl))
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
installed size is  6.2Mb
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Namespaces in Imports field not imported from:
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  ‘gridExtra’ ‘kableExtra’ ‘knitr’ ‘readr’ ‘reshape2’ ‘rmarkdown’
  ‘shinydisconnect’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
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installed size is 23.2Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘INLA’
installed size is 65.4Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
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    libs   2.4Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   6.4Mb
installed size is 27.6Mb
  sub-directories of 1Mb or more:
    libs  26.0Mb
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
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Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
installed size is 10.6Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘StrathE2E2examples’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘bnlearn’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ks’
  All declared Imports should be used.
installed size is 13.1Mb
  sub-directories of 1Mb or more:
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    libs  10.2Mb
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 34.7Mb
  sub-directories of 1Mb or more:
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installed size is  9.7Mb
  sub-directories of 1Mb or more:
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    libs   1.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘STRaitRazoR’
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
efpFunctional: multiple local function definitions for ‘plotProcess’
  with different formal arguments
mefp.efp: multiple local function definitions for ‘computeEmpProc’ with
  different formal arguments
installed size is  5.7Mb
  sub-directories of 1Mb or more:
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installed size is 12.2Mb
  sub-directories of 1Mb or more:
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  ‘purrr’ ‘shinyjs’
  All declared Imports should be used.
Missing or unexported objects:
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Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rmd’ using rmarkdown

Quitting from lines 139-147 [unnamed-chunk-5] (vignette.Rmd)
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
'gsvaParam' is not an exported object from 'namespace:GSVA'
--- failed re-building ‘vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘tidyselect’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 78 marked UTF-8 strings
Package suggested but not available for checking: ‘INLA’
installed size is  5.9Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘pROC’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘learnr’
  All declared Imports should be used.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is  8.0Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘BiocParallel’
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is  8.3Mb
  sub-directories of 1Mb or more:
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installed size is 51.0Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    doc    2.5Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
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Package suggested but not available for checking: ‘gurobi’
installed size is  9.9Mb
  sub-directories of 1Mb or more:
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Packages suggested but not available for checking:
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Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   2.3Mb
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Namespace in Imports field not imported from: ‘quadprog’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 14.8Mb
  sub-directories of 1Mb or more:
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    libs  13.0Mb
'LazyData' is specified without a 'data' directory
installed size is 63.6Mb
  sub-directories of 1Mb or more:
    libs  63.0Mb
GNU make is a SystemRequirements.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    help   1.0Mb
    libs   7.3Mb
'LazyData' is specified without a 'data' directory
installed size is 44.5Mb
  sub-directories of 1Mb or more:
    libs  44.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘swephRdata’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Packages suggested but not available for checking: 'sylly.de', 'sylly.es'
'LazyData' is specified without a 'data' directory
installed size is 45.7Mb
  sub-directories of 1Mb or more:
    libs  44.8Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
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  ‘randomForest’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
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Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 19.8Mb
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'LazyData' is specified without a 'data' directory
installed size is 21.7Mb
  sub-directories of 1Mb or more:
    libs  21.5Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
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installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
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    libs   4.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 551 marked UTF-8 strings
installed size is  6.1Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required and available but unsuitable version: ‘spork’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Note: found 81 marked UTF-8 strings
installed size is  5.1Mb
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
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Namespace in Imports field not imported from: ‘jiebaR’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 301 marked UTF-8 strings
installed size is 14.9Mb
  sub-directories of 1Mb or more:
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘tashudata’
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘microbiome’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.0Mb
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'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is 13.7Mb
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LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Undefined control sequence.
<argument>  \text 
                  {logit} \big ( E(Y) \big ) = \tau + \alpha + \delta (r - 1), 
l.172 ...g ) = \tau + \alpha + \delta (r - 1), }{}
installed size is  5.1Mb
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    tklibs   4.7Mb
Malformed Description field: should contain one or more complete sentences.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
Package suggested but not available for checking: ‘igraph’
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    doc    7.5Mb
    libs   1.7Mb
installed size is 33.8Mb
  sub-directories of 1Mb or more:
    libs  32.6Mb
GNU make is a SystemRequirements.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
Package which this enhances but not available for checking: ‘R2wd’
Package suggested but not available for checking: ‘MultiAssayExperiment’
Package suggested but not available for checking: ‘MultiAssayExperiment’
Unknown package ‘teal’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘httr’ ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs  16.5Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    libs  14.8Mb
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc    4.5Mb
    help   2.7Mb
'LazyData' is specified without a 'data' directory
installed size is 293.7Mb
  sub-directories of 1Mb or more:
    R       3.1Mb
    libs  289.3Mb
installed size is 31.5Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       8.1Mb
    tessdata  22.2Mb
Package suggested but not available for checking: ‘gurobi’
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
'LazyData' is specified without a 'data' directory
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   5.3Mb
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘mnlogit’
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   4.0Mb
Namespace in Imports field not imported from: ‘lexicon’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘forecast’ ‘parallel’ ‘tidyr’
  All declared Imports should be used.
Note: found 40 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   3.5Mb
'LazyData' is specified without a 'data' directory
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    libs  19.7Mb
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
'LazyData' is specified without a 'data' directory
installed size is 28.9Mb
  sub-directories of 1Mb or more:
    libs  28.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘ggm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    rda    7.1Mb
Package suggested but not available for checking: ‘theftdlc’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R      5.0Mb
    data   3.0Mb
Note: found 197527 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘MASS’ ‘readr’ ‘tidyverse’ ‘usethis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 84.3Mb
  sub-directories of 1Mb or more:
    libs  83.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘badger’ ‘ggplot2’ ‘lubridate’ ‘scales’ ‘xgboost’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Warning: declared S3 method 'filter.edsurvey.data.frame' not found
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mix’
  All declared Imports should be used.
Package suggested but not available for checking: ‘Rblpapi’
Package unavailable to check Rd xrefs: ‘Rblpapi’
Namespace in Imports field not imported from: ‘reticulate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘SingleR’
Warning: declared S3 method 'filter.Seurat' not found
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
installed size is 44.6Mb
  sub-directories of 1Mb or more:
    libs  43.8Mb
Note: found 34206 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc       2.0Mb
    extdata   4.5Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
Package suggested but not available for checking: ‘rrelaxiv’
installed size is 53.4Mb
  sub-directories of 1Mb or more:
    libs    15.4Mb
    tiledb  35.7Mb
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Note: found 341 marked UTF-8 strings
Namespace in Imports field not imported from: ‘lwgeom’
  All declared Imports should be used.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘org.Rn.eg.db’
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
Namespaces in Imports field not imported from:
  ‘cpp11’ ‘dplyr’ ‘magrittr’ ‘stringi’
  All declared Imports should be used.
Note: found 384749 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 90.3Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs  86.4Mb
GNU make is a SystemRequirements.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   4.6Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    examples  12.4Mb
    include    3.6Mb
installed size is 29.1Mb
  sub-directories of 1Mb or more:
    libs  28.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Rcampdf', 'tm.lexicon.GeneralInquirer'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    libs  18.8Mb
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Packages required but not available: 'EnhancedVolcano', 'Mfuzz'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Note: found 160 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘cowplot’ ‘ggplot2’ ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'RGtk2', 'gWidgets2RGtk2'
Package suggested but not available for checking: ‘gurobi’
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   8.1Mb
installed size is 211.7Mb
  sub-directories of 1Mb or more:
    R          6.1Mb
    help       1.6Mb
    include    1.8Mb
    libs     201.6Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘toscaData’
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
Note: found 100 marked Latin-1 strings
  Note: found 548 marked UTF-8 strings
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    data  13.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
Note: found 153 marked Latin-1 strings
  Note: found 108 marked UTF-8 strings
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘V8’ ‘colorspace’
  All declared Imports should be used.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    2.8Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘taxidata’
installed size is 49.1Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  46.4Mb
'LazyData' is specified without a 'data' directory
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
Package which this enhances but not available for checking: ‘fwelnet’
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Eunomia', 'CohortGenerator', 'CirceR', 'Capr'
Namespace in Imports field not imported from: ‘tree’
  All declared Imports should be used.
Packages required but not available: 'csaw', 'HiCDOC'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘TreeDistData’
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc    4.9Mb
    libs   2.3Mb
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    datasets   1.6Mb
    doc        1.3Mb
    libs       1.4Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   3.2Mb
Namespace in Imports field not imported from: ‘crul’
  All declared Imports should be used.
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    data      1.3Mb
    doc       1.3Mb
    extdata  14.8Mb
installed size is 121.2Mb
  sub-directories of 1Mb or more:
    doc     3.9Mb
    libs  116.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 38.1Mb
  sub-directories of 1Mb or more:
    libs  37.5Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'rrelaxiv', 'gurobi'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.2/triptych.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is 33.6Mb
  sub-directories of 1Mb or more:
    libs  33.4Mb
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
Namespace in Imports field not imported from: ‘tseries’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘tsglm.Rnw’ using Sweave
Error: processing vignette 'tsglm.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'tsglm.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 657 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'tsglm.Rnw'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘reticulate’ ‘tensorflow’
  All declared Imports should be used.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   9.3Mb
'LazyData' is specified without a 'data' directory
installed size is 43.8Mb
  sub-directories of 1Mb or more:
    libs  43.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘crosstalk’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   2.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 108.5Mb
  sub-directories of 1Mb or more:
    libs  107.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Warning: declared S3 method 'transform.ts_aug_awareness' not found
Warning: declared S3 method 'transform.ts_aug_awaresmooth' not found
Warning: declared S3 method 'transform.ts_aug_flip' not found
Warning: declared S3 method 'transform.ts_aug_jitter' not found
Warning: declared S3 method 'transform.ts_aug_none' not found
Warning: declared S3 method 'transform.ts_aug_shrink' not found
Warning: declared S3 method 'transform.ts_aug_stretch' not found
Warning: declared S3 method 'transform.ts_aug_wormhole' not found
Warning: declared S3 method 'transform.ts_fil_ema' not found
Warning: declared S3 method 'transform.ts_fil_hp' not found
Warning: declared S3 method 'transform.ts_fil_kalman' not found
Warning: declared S3 method 'transform.ts_fil_lowess' not found
Warning: declared S3 method 'transform.ts_fil_ma' not found
Warning: declared S3 method 'transform.ts_fil_none' not found
Warning: declared S3 method 'transform.ts_fil_qes' not found
Warning: declared S3 method 'transform.ts_fil_recursive' not found
Warning: declared S3 method 'transform.ts_fil_seas_adj' not found
Warning: declared S3 method 'transform.ts_fil_ses' not found
Warning: declared S3 method 'transform.ts_fil_smooth' not found
Warning: declared S3 method 'transform.ts_fil_spline' not found
Warning: declared S3 method 'transform.ts_fil_winsor' not found
Warning: declared S3 method 'transform.ts_norm_none' not found
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘EMD’ ‘vars’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 34 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘sl3’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘lifecycle’
  All declared Imports should be used.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc     4.5Mb
    ubinc   2.0Mb
installed size is 106.5Mb
  sub-directories of 1Mb or more:
    R       2.1Mb
    doc     1.0Mb
    libs  103.1Mb
GNU make is a SystemRequirements.
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    libs  19.4Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data       1.1Mb
    doc        1.4Mb
    shinyapp   4.9Mb
Note: found 2 marked UTF-8 strings
installed size is 27.7Mb
  sub-directories of 1Mb or more:
    doc         1.4Mb
    dummydata   1.4Mb
    libs       23.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    help   4.4Mb
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘extraDistr’ ‘logitnorm’ ‘nakagami’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 51.9Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    1.4Mb
    libs  47.5Mb
GNU make is a SystemRequirements.
Note: found 3347 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   7.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘USA.state.boundaries.data’
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   3.8Mb
Namespace in Imports field not imported from: ‘tsibble’
  All declared Imports should be used.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   7.0Mb
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Namespaces in Imports field not imported from:
  ‘RCurl’ ‘stringdist’ ‘utils’
  All declared Imports should be used.
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
installed size is 38.2Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  36.2Mb
Package required and available but unsuitable version: ‘utils’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'vaers', 'vaersND'
Packages suggested but not available for checking: 'vaers', 'vaersND'
'LazyData' is specified without a 'data' directory
installed size is 25.2Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs  22.8Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   8.7Mb
Namespace in Imports field not imported from: ‘Cairo’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘BBmisc’ ‘badger’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
installed size is 271.2Mb
  sub-directories of 1Mb or more:
    extdata    2.8Mb
    libs     267.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
Namespace in Imports field not imported from: ‘rio’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
'LazyData' is specified without a 'data' directory
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
GNU make is a SystemRequirements.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    doc   7.5Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘pander’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘foreach’ ‘iterators’ ‘maps’ ‘spam’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Missing link or links in documentation object 'bigamma.mckay.Rd':
  ‘[VGAM]{gammaff.mm}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    R      5.1Mb
    help   3.2Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Note: found 2 marked UTF-8 strings
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Note: found 468 marked UTF-8 strings
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘readr’ ‘uuid’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘mclust’ ‘rlang’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   1.0Mb
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Note: found 2754 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 51.2Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  49.5Mb
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    help          1.3Mb
    htmlwidgets   5.2Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘reshape2’
  All declared Imports should be used.
installed size is 31.9Mb
  sub-directories of 1Mb or more:
    libs  31.3Mb
GNU make is a SystemRequirements.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    doc           2.0Mb
    htmlwidgets   6.9Mb
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
Namespace in Imports field not imported from: ‘rpart’
  All declared Imports should be used.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc       5.4Mb
    extdata   1.1Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
installed size is 31.4Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     29.5Mb
GNU make is a SystemRequirements.
installed size is 55.3Mb
  sub-directories of 1Mb or more:
    libs  54.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    extdata   8.4Mb
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
Namespace in Imports field not imported from: ‘flexsurv’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘EnvStats’ ‘shiny’ ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘changing_default_parameters.Rmd’ using rmarkdown
--- finished re-building ‘changing_default_parameters.Rmd’

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

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

Quitting from lines 68-71 [unnamed-chunk-2] (process_bouts.Rmd)
Error: processing vignette 'process_bouts.Rmd' failed with diagnostics:
'origin' must be supplied
--- failed re-building ‘process_bouts.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 98.0Mb
  sub-directories of 1Mb or more:
    libs  96.7Mb
GNU make is a SystemRequirements.
Running ‘testthat.R’ [58s/92s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  19: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
  20: test_code(test = NULL, code = exprs, env = env, default_reporter = StopReporter$new())
  21: source_file(path, env = env(env), desc = desc, error_call = error_call)
  22: FUN(X[[i]], ...)
  23: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
  24: doTryCatch(return(expr), name, parentenv, handler)
  25: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  26: tryCatchList(expr, classes, parentenv, handlers)
  27: tryCatch(code, testthat_abort_reporter = function(cnd) {    cat(conditionMessage(cnd), "\n")    NULL})
  28: with_reporter(reporters$multi, lapply(test_paths, test_one_file,     env = env, desc = desc, error_call = error_call))
  29: test_files_serial(test_dir = test_dir, test_package = test_package,     test_paths = test_paths, load_helpers = load_helpers, reporter = reporter,     env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     desc = desc, load_package = load_package, error_call = error_call)
  30: test_files(test_dir = path, test_paths = test_paths, test_package = package,     reporter = reporter, load_helpers = load_helpers, env = env,     stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     load_package = load_package, parallel = parallel)
  31: test_dir("testthat", package = package, reporter = reporter,     ..., load_package = "installed")
  32: test_check("wallace")
  An irrecoverable exception occurred. R is aborting now ...
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘WRS2’ ‘ggplot2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘flextable’
  All declared Imports should be used.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   6.3Mb
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
Note: found 3133 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘prepr’
'LazyData' is specified without a 'data' directory
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    client   9.4Mb
    doc      1.0Mb
Namespaces in Imports field not imported from:
  ‘shiny’ ‘tidyselect’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 29.4Mb
  sub-directories of 1Mb or more:
    libs  29.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  10.3Mb
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   1.5Mb
Note: found 4102 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Note: found 933 marked UTF-8 strings
Warning in initDict() :
  cannot find WordNet 'dict' directory: please set the environment variable WNHOME to its parent

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sna’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   6.6Mb
Malformed Description field: should contain one or more complete sentences.
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    data  12.7Mb
Malformed Description field: should contain one or more complete sentences.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    data  11.2Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    data  11.4Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data  11.3Mb
installed size is 40.7Mb
  sub-directories of 1Mb or more:
    libs  39.8Mb
Namespaces in Imports field not imported from:
  ‘fdadensity’ ‘locfit’ ‘locpol’ ‘modeest’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
Package suggested but not available for checking: ‘ROTS’
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc       3.5Mb
    extdata   2.5Mb
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    help   1.9Mb
    libs   1.3Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magrittr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 54.1Mb
  sub-directories of 1Mb or more:
    libs  53.2Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 31.0Mb
  sub-directories of 1Mb or more:
    java  28.5Mb
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘qpdf’ ‘rlang’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RCurl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tcltk2’
  All declared Imports should be used.
installed size is 25.7Mb
  sub-directories of 1Mb or more:
    libs  25.3Mb
'LazyData' is specified without a 'data' directory
Note: found 268 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package required and available but unsuitable version: ‘spork’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
installed size is 43.0Mb
  sub-directories of 1Mb or more:
    libs  42.7Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is 42.1Mb
  sub-directories of 1Mb or more:
    libs  41.8Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘spelling’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   4.5Mb
Package suggested but not available for checking: ‘RNRCS’
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Note: found 47 marked UTF-8 strings
Note: found 5 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 40.6Mb
  sub-directories of 1Mb or more:
    libs  40.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘ggplot2’ ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs  10.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    include  12.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    htmlwidgets  11.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    R  13.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following problems:
errorevol_ranking_vector_IW.Rd:68:38: Warning: nested emphasis <code>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc   7.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    data   2.9Mb
    libs   1.2Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data   9.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    tutorials   5.5Mb
'LazyData' is specified without a 'data' directory
Package required but not available: 'cnmap'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
Package which this enhances but not available for checking: 'asreml'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    ShinyGR   4.3Mb
    doc       3.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Encountered the following conversion/validation errors:
absindex.Rd:110: condition must be plain text
feemscatter.Rd:47: condition must be plain text
write.openfluor.Rd:43: condition must be plain text
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following apparent S3 methods exported but not registered:
  print.amAlleleFreq print.amDataset
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'metaboliteIDmapping'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 35.3Mb
  sub-directories of 1Mb or more:
    R  35.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    documents     2.4Mb
    libs          1.1Mb
    screenshots   1.6Mb
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    extdata   5.4Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   1.6Mb
    doc    1.8Mb
Package suggested but not available for checking: 'arcgisbinding'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Warning: corrupt .drectve at end of def file
See 'd:/Rcompile/CRANpkg/local/4.2/arcpbf.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    help   1.1Mb
Packages suggested but not available for checking:
  'sfit', 'expectile', 'HaarSeg', 'mpcbs'
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
'LazyData' is specified without a 'data' directory
installed size is 43.3Mb
  sub-directories of 1Mb or more:
    R      4.3Mb
    libs  38.4Mb
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    bin   11.8Mb
    misc   2.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    include   6.5Mb
Package which this enhances but not available for checking: 'asreml'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'asteRiskData'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   1.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [7s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(atrrr)
  > 
  > test_check("atrrr")
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 167 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • !dir.exists(tools::R_user_dir("atrrr", "cache")) is TRUE (2):
    'test-convert.R:6:3', 'test-convert.R:16:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-actors.R:17:3'): user info pagination ──────────────────────────
  Error in `basename(req$url)`: path too long
  Backtrace:
       ▆
    1. ├─testthat::expect_equal(nrow(get_user_info(actor = actors)), 75L) at test-actors.R:17:3
    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─base::nrow(get_user_info(actor = actors))
    5. └─atrrr::get_user_info(actor = actors)
    6.   ├─base::append(...)
    7.   ├─purrr::pluck(...)
    8.   │ └─purrr:::pluck_raw(.x, list2(...), .default = .default)
    9.   ├─base::do.call(...)
   10.   └─atrrr (local) `<fn>`(`<chr>`, .token = NULL, .return = "json")
   11.     └─atrrr:::make_request(...)
   12.       └─httr2::req_perform(...)
   13.         └─atrrr (local) mock(req)
   14.           ├─base::sub("\\?.*", "", basename(req$url)) at D:\RCompile\CRANpkg\local\4.2\atrrr.Rcheck\tests\testthat\setup-mock.R:6:3
   15.           │ └─base::is.factor(x)
   16.           └─base::basename(req$url)
  
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 167 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 30.3Mb
  sub-directories of 1Mb or more:
    libs  29.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Warning: corrupt .drectve at end of def file
See 'd:/Rcompile/CRANpkg/local/4.2/b64.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'lixoftConnectors'
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   3.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R     2.6Mb
    doc   1.8Mb
Package suggested but not available for checking: 'fdpbandsdata'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    java   9.3Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   1.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   5.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   5.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    doc   10.8Mb
    libs   1.5Mb
Package suggested but not available for checking: 'INLA'
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
GNU make is a SystemRequirements.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
GNU make is a SystemRequirements.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    help   1.8Mb
    libs   3.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   1.6Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   2.2Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    help   6.0Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   3.7Mb
    doc    1.0Mb
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R     1.9Mb
    doc   3.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
GNU make is a SystemRequirements.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    1.4Mb
    libs   2.2Mb
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc       1.2Mb
    extdata   3.3Mb
    libs      1.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'BRugs'
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       3.6Mb
    extdata   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
GNU make is a SystemRequirements.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    java   7.7Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   3.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   1.3Mb
GNU make is a SystemRequirements.
installed size is 149.2Mb
  sub-directories of 1Mb or more:
    include  148.1Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'ffbase'
Package suggested but not available for checking: 'INLA'
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'rrelaxiv'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/bigrquerystorage.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'asreml'
Package suggested but not available for checking: 'vol2birdR'
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   2.0Mb
Running examples in 'bioRad-Ex.R' failed
The error most likely occurred in:

> ### Name: calculate_vp
> ### Title: Calculate a vertical profile ('vp') from a polar volume ('pvol')
> ###   file
> ### Aliases: calculate_vp
> 
> ### ** Examples
> 
> # Locate and read the polar volume example file
> pvolfile <- system.file("extdata", "volume.h5", package = "bioRad")
> 
> # Copy the file to a home directory with read/write permissions
> file.copy(pvolfile, "~/volume.h5")
[1] TRUE
> 
> # Calculate the profile
> vp <- calculate_vp("~/volume.h5")
Error in calculate_vp("~/volume.h5") : 
  The package "vol2birdR" is required to run `calculate_vp`.
Calls: calculate_vp -> <Anonymous>
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    help   2.6Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
    libs      1.2Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
Depends: includes the non-default packages:
  'colorspace', 'deldir', 'rgl', 'tcltk', 'tcltk2', 'tkrplot'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'colorspace'
A package should be listed in only one of these fields.
Packages in Depends field not imported from:
  'deldir' 'rgl' 'tcltk' 'tcltk2' 'tkrplot'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
install_blat: no visible global function definition for 'download.file'
install_blat: no visible global function definition for 'unzip'
Undefined global functions or variables:
  download.file unzip
Consider adding
  importFrom("utils", "download.file", "unzip")
to your NAMESPACE file.
Package suggested but not available for checking: 'cmdstanr'
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R          1.2Mb
    libs       5.2Mb
    testdata   1.5Mb
GNU make is a SystemRequirements.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    doc    1.0Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
GNU make is a SystemRequirements.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
GNU make is a SystemRequirements.
Found the following significant warnings:
  bnlearn/../fitted/fitted.h:63:4: warning: ISO C99 doesn't support unnamed structs/unions [-Wpedantic]
  fitted/fitted.h:63:4: warning: ISO C99 doesn't support unnamed structs/unions [-Wpedantic]
  inference/loglikelihood/../../fitted/fitted.h:63:4: warning: ISO C99 doesn't support unnamed structs/unions [-Wpedantic]
  inference/../fitted/fitted.h:63:4: warning: ISO C99 doesn't support unnamed structs/unions [-Wpedantic]
  inference/rinterface/../../fitted/fitted.h:63:4: warning: ISO C99 doesn't support unnamed structs/unions [-Wpedantic]
  minimal/../fitted/fitted.h:63:4: warning: ISO C99 doesn't support unnamed structs/unions [-Wpedantic]
  predict/../fitted/fitted.h:63:4: warning: ISO C99 doesn't support unnamed structs/unions [-Wpedantic]
  sanitization/../fitted/fitted.h:63:4: warning: ISO C99 doesn't support unnamed structs/unions [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.2/bnlearn.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   7.0Mb
installed size is 41.3Mb
  sub-directories of 1Mb or more:
    include  10.5Mb
    lib      30.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
GNU make is a SystemRequirements.
Packages suggested but not available for checking: 'cplexAPI', 'bestsubset'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    R     3.7Mb
    doc   3.6Mb
Package suggested but not available for checking: 'glmmADMB'
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   5.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/BRugs.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    components   1.0Mb
    fonts        2.9Mb
    lib          4.9Mb
GNU make is a SystemRequirements.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    2.8Mb
    libs   3.1Mb
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc       2.3Mb
    extdata   3.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   2.8Mb
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'ReGenesees'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc        2.2Mb
    pictures   4.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.7Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following apparent S3 methods exported but not registered:
  simulate.carms
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
S3 methods shown with full name in documentation object 'simulate.carms':
  'simulate.carms'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rnaturalearthhires'
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    www  12.1Mb
GNU make is a SystemRequirements.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 20.2Mb
  sub-directories of 1Mb or more:
    doc  19.9Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rkeops'
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  12.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages which this enhances but not available for checking:
  'CirceR', 'Capr'
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    2.0Mb
    libs   1.7Mb
Unexported objects imported by ':::' calls:
  'copula:::dCdu' 'copula:::fitCopStart'
  See the note in ?`:::` about the use of this operator.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 38.7Mb
  sub-directories of 1Mb or more:
    include  38.4Mb
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'darts'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'countreg'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
Package unavailable to check Rd xrefs: 'cmdstanr'
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    help   2.2Mb
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    data  17.9Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'entab'
'LazyData' is specified without a 'data' directory
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc       5.7Mb
    extdata   2.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    extdata   4.3Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'userfriendlyscience'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc   7.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    3.6Mb
    libs   1.0Mb
Found the following significant warnings:
  Warning: corrupt .drectve at end of def file
See 'd:/Rcompile/CRANpkg/local/4.2/clarabel.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    doc    1.9Mb
installed size is 48.6Mb
  sub-directories of 1Mb or more:
    extdata  48.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
Found the following problems:
fitEmaxB.Rd:191:38: Warning: nested emphasis <code>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'tobit1'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       3.2Mb
    extdata   1.7Mb
Package suggested but not available for checking: 'PopGenome'
Package suggested but not available for checking: 'disttree'
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'rkward'
Package which this enhances but not available for checking: 'rkward'
Package suggested but not available for checking: 'userfriendlyscience'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   2.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc       2.4Mb
    extdata   2.0Mb
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    java   6.7Mb
Package suggested but not available for checking: 'CAM'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
run_pipeline_gbq: no visible global function definition for
  'query_exec'
Undefined global functions or variables:
  query_exec
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'conosPanel', 'p2data'
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc             2.2Mb
    vignette_data   2.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'cec2005benchmark', 'cec2013'
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   3.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    extdata  17.7Mb
fishp: no visible binding for global variable 'markname'
fishp: no visible binding for global variable 'sum_chisq'
fishp: no visible binding for global variable 'sum_z'
pvalues_to_zscores: no visible binding for global variable 'markname'
tetracorr: no visible binding for global variable 'PLCORR'
Undefined global functions or variables:
  PLCORR markname sum_chisq sum_z
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc   6.7Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    extdata   2.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    2.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'BSgenome.Scerevisiae.UCSC.sacCer3'
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   6.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
Package suggested but not available for checking: 'INLA'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    doc    1.5Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   7.9Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   7.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   1.7Mb
    libs   7.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required and available but unsuitable version: 'IRanges'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following significant warnings:
  ./src/common/stddecl.h:481:4: warning: ISO C99 doesn't support unnamed structs/unions [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.2/cubature.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   5.8Mb
File 'curl/libs/x64/curl.dll':
  Found non-API call to R: 'R_new_custom_connection'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages which this enhances but not available for checking:
  'Rcplex', 'gurobi', 'rcbc'
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    doc    1.2Mb
    libs   1.2Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata       1.3Mb
    htmlwidgets   1.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'doMC'
Warning: declared S3 method 'transform.bal_oversampling' not found
Warning: declared S3 method 'transform.bal_subsampling' not found
Warning: declared S3 method 'transform.fs' not found
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
str:
  function(object, ...)
str.language:
  function(expr, name, indent)

See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.

Found the following apparent S3 methods exported but not registered:
  str.language
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    java   7.5Mb
GNU make is a SystemRequirements.
Packages required and available but unsuitable versions: 'methods', 'utils'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'SASxport'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'BRugs'
Package suggested but not available for checking: 'INLA'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.1Mb
    help   1.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc       4.8Mb
    extdata   2.1Mb
Package suggested but not available for checking: 'Rdonlp2'
Package suggested but not available for checking: 'Rdonlp2'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'RDCOMClient'
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    1.8Mb
    help   1.6Mb
    libs   1.2Mb
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data          1.8Mb
    htmlwidgets   3.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    doc  10.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rrelaxiv'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   4.2Mb
Package which this enhances but not available for checking: 'INLA'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'BOLTSSIRR'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    include  15.8Mb
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'introduction_to_dnapath.Rmd' using rmarkdown

Quitting from lines  at lines 221-224 [unnamed-chunk-8] (introduction_to_dnapath.Rmd)
Error: processing vignette 'introduction_to_dnapath.Rmd' failed with diagnostics:
Failed to collect lazy table.
Caused by error in `db_collect()`:
! Arguments in `...` must be used.
✖ Problematic argument:
• ..1 = Inf
ℹ Did you misspell an argument name?
--- failed re-building 'introduction_to_dnapath.Rmd'

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

Quitting from lines  at lines 234-239 [unnamed-chunk-17] (package_data.Rmd)
Error: processing vignette 'package_data.Rmd' failed with diagnostics:
Failed to collect lazy table.
Caused by error in `db_collect()`:
! Arguments in `...` must be used.
✖ Problematic argument:
• ..1 = Inf
ℹ Did you misspell an argument name?
--- failed re-building 'package_data.Rmd'

SUMMARY: processing the following files failed:
  'introduction_to_dnapath.Rmd' 'package_data.Rmd'

Error: Vignette re-building failed.
Execution halted
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc    6.5Mb
    libs   1.7Mb
GNU make is a SystemRequirements.
Package which this enhances but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R         2.1Mb
    data      2.0Mb
    extdata   2.3Mb
Package suggested but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    assets   2.9Mb
    doc      2.1Mb
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/dplyr.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data      1.7Mb
    extdata   3.2Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/DRviaSPCN.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    appinformation   4.1Mb
Package suggested but not available for checking: 'dsBaseClient'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    htmlwidgets   5.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 26.7Mb
  sub-directories of 1Mb or more:
    libs  26.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   5.1Mb
Package suggested but not available for checking: 'cmdstanr'
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    R      3.5Mb
    data   9.0Mb
Package unavailable to check Rd xrefs: 'cmdstanr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'lle'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    doc    1.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   1.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   1.8Mb
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    bin       3.5Mb
    extdata   1.7Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'lavaan.survey'
'LazyData' is specified without a 'data' directory
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
Package suggested but not available for checking: 'eggCountsExtra'
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    emoji_fonts   6.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    help   3.4Mb
'LazyData' is specified without a 'data' directory
checkRd: (5) ePCR.Rd:0-17: Must have a \description
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    help   2.5Mb
Package suggested but not available for checking: 'epidict'
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   1.0Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    help   2.1Mb
    libs   6.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    doc  13.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   4.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   6.0Mb
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data      2.5Mb
    doc       1.6Mb
    extdata   2.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'ExactData'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    exiftool  14.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cec2013'
'LazyData' is specified without a 'data' directory
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   5.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'exuberdata'
Package suggested but not available for checking: 'doMC'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Warning: declared S3 method 'forecast.GLARMA' not found
Warning: declared S3 method 'forecast.INGARCH' not found
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      3.5Mb
    doc    1.0Mb
    help   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    help   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    doc    9.2Mb
    help   1.8Mb
    libs   1.9Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    images   3.1Mb
    libs     1.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    doc    1.1Mb
    libs   1.1Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'coxKM'
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    data  15.7Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    Rcgi      3.1Mb
    cgi-bin   2.9Mb
.run: no visible binding for global variable 'init'
.run: no visible global function definition for 'init'
.run: no visible binding for global variable 'run'
Undefined global functions or variables:
  init run
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'NNLM'
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    libs   1.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following significant warnings:
  Warning: corrupt .drectve at end of def file
See 'd:/Rcompile/CRANpkg/local/4.2/fcl.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    doc    3.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    1.5Mb
    help   2.1Mb
    libs   1.6Mb
Unexported object imported by a ':::' call: 'fdapace:::interp2lin'
  See the note in ?`:::` about the use of this operator.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
GNU make is a SystemRequirements.
Found the following problems:
fRegress.Rd:321:38: Warning: nested emphasis <code>
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/fdrDiscreteNull.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data      1.9Mb
    extdata   2.8Mb
    libs      1.1Mb
Package suggested but not available for checking: 'MicrobeDS'
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    doc    3.0Mb
    help   1.1Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    R         4.7Mb
    doc       2.1Mb
    extdata   2.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    extdata   3.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    lib    3.0Mb
    libs   2.3Mb
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   4.0Mb
Package suggested but not available for checking: 'gridlayout'
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'reliaR', 'STAR'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'fivethirtyeightdata'
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
Package unavailable to check Rd xrefs: 'fivethirtyeightdata'
Found the following apparent S3 methods exported but not registered:
  plot.fpp
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    3.6Mb
    libs   1.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    help   2.3Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 23.6Mb
  sub-directories of 1Mb or more:
    libs  22.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    doc    9.1Mb
    libs   1.0Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R   7.0Mb
Malformed Description field: should contain one or more complete sentences.
GNU make is a SystemRequirements.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    fonts   6.6Mb
Malformed Description field: should contain one or more complete sentences.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    fonts   6.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'RandomFields'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R   5.6Mb
Packages suggested but not available for checking: 'dggrids', 'INLA'
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
    doc    1.8Mb
    libs  13.0Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'extraTrees', 'foba', 'nodeHarvest', 'obliqueRF', 'relaxo', 'rrlda'
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'FunWithNumbers-Ex.R' failed
The error most likely occurred in:

> ### Name: aliquot
> ### Title: Generate the Aliquot Sequence.
> ### Aliases: aliquot
> 
> ### ** Examples
> 
> aliquot(20)
Error in if (aliseq[j] %in% aliseq[1:(j - 1)]) { : 
  the condition has length > 1
Calls: aliquot
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    help   4.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc   7.9Mb
installed size is 33.6Mb
  sub-directories of 1Mb or more:
    doc   31.8Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      2.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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.
Package suggested but not available for checking: 'paleofire'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 76.4Mb
  sub-directories of 1Mb or more:
    L8NY18   2.3Mb
    gdal     2.8Mb
    libs    62.3Mb
    proj     7.7Mb
installed size is 73.7Mb
  sub-directories of 1Mb or more:
    gdal   2.8Mb
    libs  60.8Mb
    proj   7.7Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
Package suggested but not available for checking: 'gdxrrw'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   3.2Mb
    libs      1.1Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'genderdata'
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
Error(s) in re-building vignettes:
--- re-building 'geoAr_geofacet.Rmd' using rmarkdown
File figure/tucmap-1.png not found in resource path
Error: processing vignette 'geoAr_geofacet.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'geoAr_geofacet.Rmd'

--- re-building 'geoAr_leaflet.Rmd' using rmarkdown
File figure/map-1.png not found in resource path
Error: processing vignette 'geoAr_leaflet.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'geoAr_leaflet.Rmd'

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

SUMMARY: processing the following files failed:
  'geoAr_geofacet.Rmd' 'geoAr_leaflet.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
    libs      1.4Mb
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc       2.1Mb
    extdata   3.5Mb
Package suggested but not available for checking: 'geomarocdata'
'LazyData' is specified without a 'data' directory
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    R         9.6Mb
    extdata   2.5Mb
    help      2.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'RandomFields'

Package which this enhances but not available for checking: 'INLA'
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'RGtk2'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc       3.0Mb
    extdata   1.6Mb
    libs      1.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    doc   7.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    2.3Mb
    help   1.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'lixoftConnectors'
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    help       2.4Mb
    testdata   4.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   3.9Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   9.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc    9.5Mb
    help   1.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    Giac  17.9Mb
GNU make is a SystemRequirements.
Found the following significant warnings:
  Warning: corrupt .drectve at end of def file
See 'd:/Rcompile/CRANpkg/local/4.2/gifski.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    help   2.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.UCSC.hg18.masked',
  'BSgenome.Hsapiens.UCSC.hg19.masked'
Package suggested but not available for checking: 'doMC'
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   4.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
GNU make is a SystemRequirements.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc             1.3Mb
    libs            4.5Mb
    test_data       2.3Mb
    vignette_data   1.1Mb
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'doMC'
'LazyData' is specified without a 'data' directory
Found the following problems:
get_k_stages_adjacency_tensor.Rd:58:38: Warning: nested emphasis <code>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'gofastr-Ex.R' failed
The error most likely occurred in:

> ### Name: as_dtm
> ### Title: Coerce Various Object Into a
> ###   'DocumentTermMatrix'/'TermDocumentMatrix'
> ### Aliases: as_dtm as_tdm
> ### Keywords: documenttermmatrix, termdocumentmatrix
> 
> ### ** Examples
> 
> with(partial_republican_debates_2015,
+     as_dtm(dialogue, paste(location, element_id, sentence_id, sep = "_"))
+ )
Error:
! The `stem` argument of `dfm()` was deprecated in quanteda 3.0 and is
  now defunct.
ℹ Please use `dfm_stem()` instead.
Backtrace:
     ▆
  1. ├─base::with(...)
  2. └─base::with.default(...)
  3.   └─base::eval(substitute(expr), data, enclos = parent.frame())
  4.     └─base::eval(substitute(expr), data, enclos = parent.frame())
  5.       ├─gofastr::as_dtm(...)
  6.       └─gofastr:::as_dtm.character(...)
  7.         ├─tm::weightTfIdf(q_dtm(x, ...))
  8.         └─gofastr::q_dtm(x, ...)
  9.           ├─quanteda::convert(...)
 10.           └─quanteda::dfm(...)
 11.             └─quanteda:::check_defunct_dfm_args(names(as.list(sys.call())[-1]))
 12.               └─lifecycle::deprecate_stop(...)
 13.                 └─lifecycle:::deprecate_stop0(msg)
 14.                   └─rlang::cnd_signal(...)
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R   6.1Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    3.5Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    help   5.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    help   2.0Mb
    libs   1.2Mb
GNU make is a SystemRequirements.
accrualReport: multiple local function definitions for 'gg' with
  different formal arguments
Package suggested but not available for checking: 'doMC'
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   2.7Mb
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    extdata   5.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    4.1Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following problems:
GWASinlps.Rd:187:1: Warning: trimming empty <h4>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 267.7Mb
  sub-directories of 1Mb or more:
    R       1.5Mb
    java  264.7Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    doc    1.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs    1.0Mb
    shiny   4.3Mb
'LazyData' is specified without a 'data' directory
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    HaDeX   4.0Mb
    doc     4.0Mb
'LazyData' is specified without a 'data' directory
Warning: declared S3 method 'transform.trans_sax' not found
Warning: declared S3 method 'transform.trans_xsax' not found
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    doc    2.6Mb
    libs   1.3Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
GNU make is a SystemRequirements.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R         2.6Mb
    extdata   1.3Mb
GNU make is a SystemRequirements.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc           2.7Mb
    htmlwidgets   2.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
'LazyData' is specified without a 'data' directory
Found the following problems:
KMHFA.Rd:128:38: Warning: nested emphasis <code>


KMHFA.Rd:132:38: Warning: nested emphasis <code>


KPCA.Rd:73:38: Warning: nested emphasis <code>


KPCA.Rd:77:38: Warning: nested emphasis <code>


KPE.Rd:83:38: Warning: nested emphasis <code>


KPE.Rd:87:38: Warning: nested emphasis <code>
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   1.3Mb
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    3.7Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
Found the following significant warnings:
  Warning: corrupt .drectve at end of def file
See 'd:/Rcompile/CRANpkg/local/4.2/heck.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package which this enhances but not available for checking: 'HadoopStreaming'
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.3Mb
html_describe_con: multiple local function definitions for 'g' with
  different formal arguments
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 15.0Mb
  sub-directories of 1Mb or more:
    libs  13.8Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'glmmADMB'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    app   1.7Mb
    doc   3.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'RGtk2', 'cairoDevice'
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    doc    2.3Mb
    help   1.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'hurricaneexposuredata'
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'microViz'
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
    libs      1.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
'LazyData' is specified without a 'data' directory
Found the following problems:
baseflow.Rd:167:38: Warning: nested emphasis <code>


baseflow.Rd:171:38: Warning: nested emphasis <code>
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    extdata   5.8Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   6.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following problems:
KIALS.Rd:92:38: Warning: nested emphasis <code>


KIALS.Rd:96:38: Warning: nested emphasis <code>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'SparkR'
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    1.6Mb
    libs   1.0Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.1000genomes.hs37d5',
  'BSgenome.Mmusculus.UCSC.mm10'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'icd'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/ICDS.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'rggobi'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'IFCdata'
'LazyData' is specified without a 'data' directory
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.2Mb
    help   1.9Mb
    libs   6.4Mb
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    dlib-19.20   9.3Mb
    libs         1.4Mb
installed size is 19.6Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       3.7Mb
    extdata   1.0Mb
    include   3.0Mb
    libs      9.8Mb
installed size is 21.6Mb
  sub-directories of 1Mb or more:
    libs   10.5Mb
    share  10.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    1.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'accdata'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
logLik:
  function(object, ...)
logLik.displacement:
  function(model, ...)

See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.

Found the following apparent S3 methods exported but not registered:
  logLik.displacement
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
S3 methods shown with full name in documentation object 'logLik.displacement':
  'logLik.displacement'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
Package suggested but not available for checking: 'INLA'
Package suggested but not available for checking: 'INLA'
Package suggested but not available for checking: 'INLA'
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    doc   9.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/intrinsicFRP.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
Package unavailable to check Rd xrefs: 'INLA'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'surveyspec'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File 'iotools/libs/x64/iotools.dll':
  Found non-API calls to R: 'R_GetConnection', 'R_ReadConnection',
    'R_WriteConnection'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(iperform)
  > 
  > test_check("iperform")
  [ FAIL 5 | WARN 0 | SKIP 0 | PASS 45 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-dday.R:7:3'): dday works ─────────────────────────────────────
  dday(df, "2023-08-03", x = "x") (`actual`) not identical to 8 (`expected`).
  
    `actual`: 0
  `expected`: 8
  ── Failure ('test-dday.R:8:3'): dday works ─────────────────────────────────────
  dday(df, "2023-08-05", d = -1, x = "x") (`actual`) not identical to 12 (`expected`).
  
    `actual`:  0
  `expected`: 12
  ── Failure ('test-dday.R:9:3'): dday works ─────────────────────────────────────
  dday(df, "2023-08-05", d = 0, x = "x") (`actual`) not identical to 6 (`expected`).
  
    `actual`: 0
  `expected`: 6
  ── Failure ('test-dday.R:10:3'): dday works ────────────────────────────────────
  dday(df, "2023-08-01", d = 1, x = "x") (`actual`) not identical to 13 (`expected`).
  
    `actual`:  0
  `expected`: 13
  ── Failure ('test-ytd.R:12:3'): ytd works ──────────────────────────────────────
  ytd(df, "2023-08-01", x = "x") (`actual`) not equal to dday(df, "2023-08-01", x = "x") (`expected`).
  
    `actual`: 10
  `expected`:  0
  
  [ FAIL 5 | WARN 0 | SKIP 0 | PASS 45 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory