##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PloGO2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PloGO2_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/PloGO2.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PloGO2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PloGO2’ version ‘1.16.0’
* 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 ‘PloGO2’ can be installed ... OK
* 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 code 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 whether startup messages can be suppressed ... 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 ... NOTE
Children: no visible global function definition for ‘Ontology’
ExcelToPloGO: no visible binding for global variable ‘Term’
ExcelToPloGO: no visible binding for global variable ‘Ontology’
GOGraphWrapper: no visible global function definition for ‘Ontology’
GOParent: no visible global function definition for ‘Ontology’
GOTermList: no visible global function definition for ‘Ontology’
PloGO: no visible global function definition for ‘read.delim’
PloGO: no visible global function definition for ‘unzip’
PloGO: no visible global function definition for ‘read.csv’
PloPathway: no visible global function definition for ‘unzip’
PloPathway : <anonymous>: no visible global function definition for
  ‘read.table’
PloPathway: no visible global function definition for ‘read.csv’
abundancePlot: no visible binding for global variable ‘eps’
aggregateAbundance : <anonymous>: no visible global function definition
  for ‘Term’
aggregateAbundance : <anonymous>: no visible global function definition
  for ‘aggregate’
annotationPlot : <anonymous>: no visible global function definition for
  ‘Term’
compareAnnot: no visible global function definition for ‘fisher.test’
compareAnnot : <anonymous>: no visible global function definition for
  ‘Term’
compareAnnot: no visible global function definition for ‘p.adjust’
countAndAbundance: no visible global function definition for ‘par’
countAndAbundance: no visible global function definition for ‘barplot’
countAndAbundance: no visible global function definition for ‘axTicks’
countAndAbundance: no visible global function definition for ‘axis’
countAndAbundance: no visible global function definition for ‘title’
genAnnotationFiles: no visible global function definition for
  ‘read.csv’
genAnnotationFiles: no visible global function definition for
  ‘write.table’
genWegoFile: no visible global function definition for ‘useMart’
genWegoFile: no visible global function definition for ‘useDataset’
genWegoFile: no visible global function definition for ‘getBM’
genWegoFile: no visible global function definition for ‘aggregate’
genWegoFile: no visible global function definition for ‘write.table’
getGoID: no visible binding for global variable ‘Term’
getUniprotBatch: no visible binding for global variable ‘IDList’
inGraph: no visible global function definition for ‘nodes’
plotAbundanceBar: no visible global function definition for ‘par’
plotAbundanceBar: no visible global function definition for ‘barplot’
plotAbundanceBar: no visible global function definition for ‘rainbow’
plotAbundanceBar: no visible global function definition for ‘legend’
plotMat: no visible global function definition for ‘colorRampPalette’
plotMat : <anonymous>: no visible global function definition for ‘Term’
processAnnotFile: no visible global function definition for ‘read.csv’
processGoFile : <anonymous>: no visible global function definition for
  ‘Term’
processGoFile: no visible global function definition for ‘read.csv’
processPathFile: no visible global function definition for ‘read.csv’
read.annot.file: no visible global function definition for ‘read.table’
read.annot.file: no visible global function definition for ‘aggregate’
tabulateAnnot : <anonymous>: no visible global function definition for
  ‘Term’
writeGOannot: no visible global function definition for ‘read.csv’
writeGOannot: no visible global function definition for ‘write.csv’
writeGOannot: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  IDList Ontology Term aggregate axTicks axis barplot colorRampPalette
  eps fisher.test getBM legend nodes p.adjust par rainbow read.csv
  read.delim read.table title unzip useDataset useMart write.csv
  write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "rainbow")
  importFrom("graphics", "axTicks", "axis", "barplot", "legend", "par",
             "title")
  importFrom("stats", "aggregate", "fisher.test", "p.adjust")
  importFrom("utils", "read.csv", "read.delim", "read.table", "unzip",
             "write.csv", "write.table")
to your NAMESPACE file.
* 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 R/sysdata.rda ... 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
PloGO             41.693  3.091  44.923
abundancePlot     22.532  0.928  23.507
processAnnotation 21.279  1.141  22.481
writeAnnotation   20.386  1.156  21.608
getGoID           18.066  0.079  18.178
processGoFile     10.506  0.224  10.754
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/PloGO2.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL PloGO2
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘PloGO2’ ...
** using staged installation
** R
** 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 in fun(libname, pkgname) :
  Package 'PloGO2' is deprecated and will be removed from Bioconductor
  version 3.20
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'PloGO2' is deprecated and will be removed from Bioconductor
  version 3.20
** testing if installed package keeps a record of temporary installation path
* DONE (PloGO2)