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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PloGO2.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings PloGO2_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/PloGO2.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'PloGO2/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PloGO2' version '1.6.0'
* 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 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... 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 files in 'vignettes' ... NOTE
The following files look like leftovers/mistakes:
  'Rplots.pdf'
Please remove them from your package.
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
PloGO             41.58   0.28   42.07
abundancePlot     19.80   1.33   21.37
writeAnnotation   19.63   0.02   19.64
getGoID           18.71   0.00   18.70
processAnnotation 17.76   0.09   17.87
processGoFile      9.85   0.03    9.88
ExcelToPloPathway  4.92   0.95    6.11
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
PloGO             37.57   0.30   37.87
getGoID           23.95   0.05   24.00
writeAnnotation   21.08   0.07   21.16
processAnnotation 20.41   0.10   20.52
abundancePlot     19.11   1.11   20.22
processGoFile     11.23   0.08   11.31
ExcelToPloPathway  5.59   0.82    6.86
* 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 ... OK
* DONE

Status: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/PloGO2.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/PloGO2_1.6.0.tar.gz && rm -rf PloGO2.buildbin-libdir && mkdir PloGO2.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PloGO2.buildbin-libdir PloGO2_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL PloGO2_1.6.0.zip && rm PloGO2_1.6.0.tar.gz PloGO2_1.6.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 69 1097k   69  768k    0     0   978k      0  0:00:01 --:--:--  0:00:01  978k
100 1097k  100 1097k    0     0  1126k      0 --:--:-- --:--:-- --:--:-- 1125k

install for i386

* installing *source* package 'PloGO2' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'PloGO2'
    finding HTML links ... done
    ExcelToPloGO                            html  
    ExcelToPloPathway                       html  
    GOTermList                              html  
    PloGO                                   html  
    PloPathway                              html  
    abundancePlot                           html  
    annotationPlot                          html  
    compareAnnot                            html  
    genAnnotationFiles                      html  
    genWegoFile                             html  
    getGoID                                 html  
    plotAbundanceBar                        html  
    printSummary                            html  
    processAnnotation                       html  
    processGoFile                           html  
    processPathFile                         html  
    read.annot.file                         html  
    writeAnnotation                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'PloGO2' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PloGO2' as PloGO2_1.6.0.zip
* DONE (PloGO2)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'PloGO2' successfully unpacked and MD5 sums checked