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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:caOmicsV.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings caOmicsV_1.26.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/caOmicsV.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘caOmicsV/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘caOmicsV’ version ‘1.26.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘caOmicsV’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'caOmicsV' is deprecated and will be removed from Bioconductor
See ‘/Users/biocbuild/bbs-3.15-bioc/meat/caOmicsV.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
bioNetLegend             9.186  0.457   9.746
plotBioNetCircos         8.540  0.378   8.951
plotBioNetHeatmap        6.144  0.233   6.392
drawBioNetNodeBackground 5.396  0.222   5.642
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... ERROR
Rd conversion errors:
Converting parsed Rd's to LaTeX ..Warning in nm[isAlias] <- sapply(Rd[isAlias], as.character) :
  number of items to replace is not a multiple of replacement length
Error in writeAlias(section, tag) : alias:
‘

    getBioMatrixBasePositions

    getBioMatrixColumnPadding

    getBioMatrixDataAreaWidth

    getBioMatrixGeneLabelWidth

    getBioMatrixGeneNumber

    getBioMatrixLegendHeight

    getBioMatrixPhenotypeNumber

    getBioMatrixPlotAreaHeigth

    getBioMatrixPlotAreaWidth

    getBioMatrixRemarkWidth

    getBioMatrixSummaryWidth

    getBioMatrixRowPadding

    getBioMatrixSampleHeight

    getBioMatrixSampleIDHeight

    getBioMatrixSampleNumber

    getBioMatrixSampleWidth
’
is not one line
* DONE

Status: 1 ERROR, 1 WARNING
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/caOmicsV.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL caOmicsV
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘caOmicsV’ ...
** using staged installation
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'caOmicsV' is deprecated and will be removed from Bioconductor
  version 3.16
** testing if installed package can be loaded from final location
Warning: Package 'caOmicsV' is deprecated and will be removed from Bioconductor
  version 3.16
** testing if installed package keeps a record of temporary installation path
* DONE (caOmicsV)