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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:oposSOM.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings oposSOM_2.13.1.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/oposSOM.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '2.13.1'
* 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 18.5Mb
  sub-directories of 1Mb or more:
    data  17.0Mb
* 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 ... 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 x64 is not available
File 'D:/biocbuild/bbs-3.15-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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
oposSOM-package 132.05  21.16   79.50
opossom.run      42.06   2.62   50.68
* 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
  'D:/biocbuild/bbs-3.15-bioc/meat/oposSOM.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL oposSOM
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'oposSOM' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c DeltaMatrix.cpp -o DeltaMatrix.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c DistanceCalculator.cpp -o DistanceCalculator.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c NeighborhoodMatrix.cpp -o NeighborhoodMatrix.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c RcppExports.cpp -o RcppExports.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o oposSOM.dll tmp.def DeltaMatrix.o DistanceCalculator.o NeighborhoodMatrix.o RcppExports.o -LD:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-oposSOM/00new/oposSOM/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'oposSOM'
    finding HTML links ... done
    oposSOM-package                         html  
    opossom.genesets                        html  
    opossom.new                             html  
    opossom.run                             html  
    opossom.tissues                         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
* DONE (oposSOM)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'puma' is missing or broken
 done