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### Running command:
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###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:oposSOM.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings oposSOM_2.12.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/oposSOM.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 'oposSOM/DESCRIPTION' ... OK
* this is package 'oposSOM' version '2.12.0'
* 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 'oposSOM' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 19.6Mb
  sub-directories of 1Mb or more:
    data  17.0Mb
    libs   2.1Mb
* 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 ... NOTE
Unexported object imported by a ':::' call: 'tools:::makeLazyLoadDB'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... WARNING
plot:
  function(x, ...)
plot.psf.pathway.keggrest:
  function(kegg.pathway, signal.values, signal.values.lim, main,
           highlight.genes, color.palette)

plot:
  function(x, ...)
plot.psf.titlepage:
  function(env, psf.object, signal.values, bar.colors)

sort:
  function(x, decreasing, ...)
sort.label:
  function(x)

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

Found the following apparent S3 methods exported but not registered:
  plot.psf.pathway.keggrest plot.psf.titlepage sort.label
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
psf.overview.heatmaps: warning in heatmap(x =
  log1p(log1p(mean.psf.matrix)), cex.main = 2, col =
  color.palette(1000), scale = "r", mar = c(10, 20), ColSideColors =
  group.colors, cexDend = 0.6): partial argument match of 'mar' to
  'margins'
psf.overview.heatmaps: warning in heatmap(x =
  log1p(log1p(mean.psf.matrix)), cex.main = 2, col =
  color.palette(1000), scale = "r", mar = c(10, 20), ColSideColors =
  group.colors, Colv = NA, cexDend = 0.6): partial argument match of
  'mar' to 'margins'
Smooth.Matrix: no visible binding for global variable 'v'
modules.relations: no visible global function definition for
  'graph.empty'
modules.relations: no visible global function definition for
  'add_edges'
pipeline.PSFcalculation: no visible binding for global variable
  'kegg.collection'
pipeline.checkInputParameters: no visible binding for global variable
  'preferences'
pipeline.diffExpressionStatistics : <anonymous>: no visible global
  function definition for 't.test'
pipeline.differenceAnalyses : <anonymous>: no visible global function
  definition for 't.test'
pipeline.groupAnalysis : <anonymous>: no visible global function
  definition for 't.test'
pipeline.htmlPsfAnalysis: no visible binding for global variable
  'kegg.collection'
pipeline.prepareAnnotation: no visible binding for global variable
  'opossom.genesets'
pipeline.sampleSimilarityAnalysisCor: no visible global function
  definition for 'get.edgelist'
pipeline.topologyProfiles: no visible binding for global variable
  'group.labels'
plot.psf.pathway.keggrest: no visible global function definition for
  'rasterImage'
psf.report.sheets: no visible binding for global variable 'kegg.data'
Undefined global functions or variables:
  add_edges get.edgelist graph.empty group.labels kegg.collection
  kegg.data opossom.genesets preferences rasterImage t.test v
Consider adding
  importFrom("graphics", "rasterImage")
  importFrom("stats", "t.test")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'GeneSet.Fisher' 'GeneSet.maxmean' 'Get.Running.Average'
  'Quantile.Normalization' 'Sample.GSZ' 'Smooth.Matrix'
  '_oposSOM_calculateDelta' '_oposSOM_calculateEuclideanDistances'
  '_oposSOM_calculateNeighborhoodMatrix'
  '_oposSOM_matrixToCodebookMatrix' 'biomart.available'
  'calculateDelta' 'calculateEuclideanDistances'
  'calculateNeighborhoodMatrix' 'circle' 'col.pix'
  'color.palette.discrete' 'color.palette.heatmaps'
  'color.palette.portraits' 'get.beta.statistic' 'get.neighbors'
  'heatmap' 'heatmap.A4' 'matrixToCodebookMatrix' 'modules.CSV.sheets'
  'modules.chromosomes' 'modules.profiles' 'modules.relations'
  'modules.report.sheets' 'newProgressBar' 'pathway.expression.mapping'
  'pipeline.PSFcalculation' 'pipeline.PSFoutput'
  'pipeline.affymetrixQualityCheck' 'pipeline.cancerHallmarks'
  'pipeline.checkInputParameters'
  'pipeline.chromosomeExpressionReports'
  'pipeline.detectEnsemblDataset' 'pipeline.detectSpotsModules'
  'pipeline.detectSpotsSamples' 'pipeline.diffExpressionStatistics'
  'pipeline.differenceAnalyses' 'pipeline.entropyProfiles'
  'pipeline.geneLists' 'pipeline.generateSOM'
  'pipeline.genesetOverviews' 'pipeline.genesetProfilesAndMaps'
  'pipeline.genesetStatisticModules' 'pipeline.genesetStatisticSamples'
  'pipeline.groupAnalysis' 'pipeline.groupAssignment'
  'pipeline.groupSpecificGenesets' 'pipeline.htmlDifferencesSummary'
  'pipeline.htmlGenesetAnalysis' 'pipeline.htmlGroupSummary'
  'pipeline.htmlModuleSummary' 'pipeline.htmlPsfAnalysis'
  'pipeline.htmlSampleSummary' 'pipeline.htmlSummary'
  'pipeline.moduleCorrelationMap' 'pipeline.patAssignment'
  'pipeline.prepareAnnotation' 'pipeline.prepareIndata'
  'pipeline.qualityCheck' 'pipeline.sampleExpressionPortraits'
  'pipeline.sampleSimilarityAnalysisCor'
  'pipeline.sampleSimilarityAnalysisED'
  'pipeline.sampleSimilarityAnalysisICA'
  'pipeline.sampleSimilarityAnalysisSOM' 'pipeline.summarySheetsGroups'
  'pipeline.summarySheetsModules' 'pipeline.summarySheetsPATs'
  'pipeline.summarySheetsSamples' 'pipeline.supportingMaps'
  'pipeline.topologyProfiles' 'plot.psf.pathway.keggrest'
  'plot.psf.titlepage' 'psf.flow' 'psf.overview.heatmaps'
  'psf.report.sheets' 'radarchart' 'som.linear.init'
  'som.linear.init.subdata' 'som.training' 'som.training.phase'
  'sort.label' 'util.call' 'util.cat' 'util.fatal' 'util.info'
  'util.load' 'util.log' 'util.progress' 'util.progress.terminate'
  'util.save' 'util.warn' 'workspace.check'
Undocumented data sets:
  'hsa03320.RData' 'hsa04010.RData' 'hsa04012.RData' 'hsa04014.RData'
  'hsa04015.RData' 'hsa04020.RData' 'hsa04022.RData' 'hsa04024.RData'
  'hsa04062.RData' 'hsa04064.RData' 'hsa04066.RData' 'hsa04068.RData'
  'hsa04070.RData' 'hsa04071.RData' 'hsa04072.RData' 'hsa04115.RData'
  'hsa04150.RData' 'hsa04151.RData' 'hsa04152.RData' 'hsa04261.RData'
  'hsa04310.RData' 'hsa04330.RData' 'hsa04340.RData' 'hsa04350.RData'
  'hsa04370.RData' 'hsa04371.RData' 'hsa04390.RData' 'hsa04392.RData'
  'hsa04550.RData' 'hsa04620.RData' 'hsa04621.RData' 'hsa04622.RData'
  'hsa04625.RData' 'hsa04630.RData' 'hsa04657.RData' 'hsa04660.RData'
  'hsa04662.RData' 'hsa04664.RData' 'hsa04668.RData' 'hsa04722.RData'
  'hsa04723.RData' 'hsa04910.RData' 'hsa04912.RData' 'hsa04915.RData'
  'hsa04917.RData' 'hsa04919.RData' 'hsa04920.RData' 'hsa04921.RData'
  'hsa04922.RData' 'hsa04926.RData' 'hsa04933.RData' 'hsa05120.RData'
  'kegg.collection.RData'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... WARNING
Found the following file(s) containing GNU extensions:
  src/Makevars
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif, .NOTPARALLEL See section 'Writing portable
packages' in the 'Writing R Extensions' manual.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/oposSOM/libs/i386/oposSOM.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/oposSOM/libs/x64/oposSOM.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (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. 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.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
oposSOM-package 178.69   9.09   69.41
opossom.run      72.03   2.13   72.92
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
oposSOM-package 184.60  15.67   77.25
opossom.run      74.02   3.61   91.42
* 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: 3 WARNINGs, 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/oposSOM.Rcheck/00check.log'
for details.