Package: oposSOM

Version: 2.0.0

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:oposSOM.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings oposSOM_2.0.0.tar.gz

StartedAt: 2019-04-13 04:18:43 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 04:45:30 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 1606.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: oposSOM.Rcheck

Warnings: 1

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###
### Running command:
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###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:oposSOM.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings oposSOM_2.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/oposSOM.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '2.0.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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  5.2Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    libs   1.5Mb
* 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
GeneSet.Fisher : fn: no visible global function definition for
  'fisher.test'
Smooth.Matrix: no visible binding for global variable 'v'
biomart.available: no visible binding for global variable 'preferences'
get.beta.statistic: no visible global function definition for 'pbeta'
heatmap: no visible binding for global variable 'dist'
heatmap: no visible binding for global variable 'hclust'
heatmap : <anonymous>: no visible global function definition for
  'reorder'
heatmap: no visible global function definition for 'as.dendrogram'
heatmap: no visible global function definition for 'order.dendrogram'
heatmap: no visible binding for global variable 'sd'
heatmap: no visible global function definition for 'par'
heatmap: no visible global function definition for 'layout'
heatmap: no visible global function definition for 'image'
heatmap: no visible global function definition for 'axis'
heatmap: no visible global function definition for 'mtext'
heatmap: no visible global function definition for 'plot'
heatmap: no visible global function definition for 'frame'
heatmap: no visible global function definition for 'title'
modules.CSV.sheets : <anonymous>: no visible binding for global
  variable 'indata'
modules.CSV.sheets : <anonymous>: no visible global function definition
  for 'cor'
modules.CSV.sheets: no visible binding for global variable 'indata'
modules.CSV.sheets: no visible global function definition for 'pt'
modules.CSV.sheets: no visible binding for global variable 'gene.info'
modules.CSV.sheets: no visible binding for global variable
  'indata.gene.mean'
modules.CSV.sheets: no visible binding for global variable 'sd'
modules.CSV.sheets: no visible global function definition for
  'write.csv2'
modules.chromosomes: no visible binding for global variable
  'chromosome.list'
modules.chromosomes: no visible global function definition for 'pdf'
modules.chromosomes : <anonymous>: no visible binding for global
  variable 'chromosome.list'
modules.chromosomes: no visible global function definition for
  'colorRampPalette'
modules.chromosomes: no visible binding for global variable 'head'
modules.chromosomes: no visible global function definition for 'par'
modules.chromosomes: no visible global function definition for 'image'
modules.chromosomes: no visible global function definition for 'title'
modules.chromosomes: no visible global function definition for 'box'
modules.chromosomes: no visible global function definition for 'abline'
modules.chromosomes: no visible global function definition for 'axis'
modules.chromosomes: no visible global function definition for 'layout'
modules.chromosomes: no visible global function definition for 'plot'
modules.chromosomes: no visible global function definition for 'text'
modules.chromosomes: no visible global function definition for
  'dev.off'
modules.profiles: no visible global function definition for 'sd'
modules.profiles: no visible global function definition for 'pdf'
modules.profiles: no visible global function definition for 'layout'
modules.profiles: no visible global function definition for 'par'
modules.profiles: no visible global function definition for 'image'
modules.profiles: no visible binding for global variable 'preferences'
modules.profiles: no visible global function definition for 'axis'
modules.profiles: no visible global function definition for 'box'
modules.profiles: no visible global function definition for 'barplot'
modules.profiles: no visible binding for global variable 'group.colors'
modules.profiles: no visible binding for global variable 'indata'
modules.profiles: no visible global function definition for 'abline'
modules.profiles: no visible binding for global variable 'group.labels'
modules.profiles: no visible global function definition for 'text'
modules.profiles: no visible binding for global variable
  'groupwise.group.colors'
modules.profiles: no visible global function definition for 'plot'
modules.profiles: no visible global function definition for 'boxplot'
modules.profiles: no visible global function definition for 'dev.off'
modules.relations: no visible global function definition for 'sd'
modules.relations: no visible global function definition for 'pdf'
modules.relations: no visible global function definition for 'cor'
modules.relations: no visible global function definition for 'layout'
modules.relations: no visible global function definition for 'par'
modules.relations: no visible global function definition for 'image'
modules.relations: no visible binding for global variable 'preferences'
modules.relations: no visible global function definition for 'box'
modules.relations: no visible global function definition for 'plot'
modules.relations: no visible global function definition for 'legend'
modules.relations : <anonymous>: no visible binding for global variable
  'group.labels'
modules.relations : <anonymous> : <anonymous>: no visible binding for
  global variable 'group.labels'
modules.relations : <anonymous> : <anonymous>: no visible binding for
  global variable 'indata'
modules.relations: no visible global function definition for
  'graph.empty'
modules.relations: no visible global function definition for
  'add_edges'
modules.relations: no visible binding for global variable
  'groupwise.group.colors'
modules.relations: no visible global function definition for 'title'
modules.relations: no visible binding for global variable
  'group.labels'
modules.relations: no visible global function definition for 'frame'
modules.relations: no visible global function definition for 'text'
modules.relations: no visible global function definition for 'barplot'
modules.relations: no visible global function definition for 'dev.off'
modules.report.sheets: no visible global function definition for 'pdf'
modules.report.sheets: no visible global function definition for
  'layout'
modules.report.sheets: no visible global function definition for 'par'
modules.report.sheets: no visible global function definition for
  'color.palette.portraits'
modules.report.sheets: no visible global function definition for
  'colorRampPalette'
modules.report.sheets: no visible global function definition for
  'image'
modules.report.sheets: no visible binding for global variable
  'preferences'
modules.report.sheets: no visible global function definition for
  'mtext'
modules.report.sheets: no visible global function definition for 'box'
modules.report.sheets: no visible global function definition for 'plot'
modules.report.sheets: no visible global function definition for
  'points'
modules.report.sheets: no visible global function definition for 'text'
modules.report.sheets : <anonymous>: no visible global function
  definition for 'head'
modules.report.sheets: no visible global function definition for
  'legend'
modules.report.sheets: no visible binding for global variable 'indata'
modules.report.sheets: no visible global function definition for
  'color.palette.heatmaps'
modules.report.sheets: no visible global function definition for 'axis'
modules.report.sheets: no visible binding for global variable
  'group.labels'
modules.report.sheets: no visible binding for global variable
  'group.colors'
modules.report.sheets: no visible global function definition for
  'frame'
modules.report.sheets: no visible global function definition for 'sd'
modules.report.sheets: no visible global function definition for 'cor'
modules.report.sheets: no visible binding for global variable
  'metadata'
modules.report.sheets: no visible global function definition for
  'barplot'
modules.report.sheets : <anonymous>: no visible binding for global
  variable 'indata'
modules.report.sheets : <anonymous>: no visible global function
  definition for 'cor'
modules.report.sheets: no visible global function definition for 'rect'
modules.report.sheets: no visible binding for global variable
  'gene.info'
modules.report.sheets: no visible binding for global variable
  'gs.def.list'
modules.report.sheets : <anonymous>: no visible binding for global
  variable 'gene.info'
modules.report.sheets: no visible global function definition for 'hist'
modules.report.sheets: no visible global function definition for
  'abline'
modules.report.sheets: no visible global function definition for
  'lines'
modules.report.sheets: no visible global function definition for
  'dev.off'
newProgressBar : up3: no visible global function definition for
  'flush.console'
newProgressBar : kill: no visible global function definition for
  'flush.console'
opossom.new: no visible global function definition for 'modifyList'
opossom.run: no visible global function definition for 'sessionInfo'
pipeline.affymetrixQualityCheck: no visible binding for global variable
  'indata'
pipeline.affymetrixQualityCheck: no visible global function definition
  for 'par'
pipeline.affymetrixQualityCheck: no visible global function definition
  for 'barplot'
pipeline.affymetrixQualityCheck: no visible binding for global variable
  'group.colors'
pipeline.affymetrixQualityCheck: no visible global function definition
  for 'box'
pipeline.affymetrixQualityCheck: no visible binding for global variable
  'group.labels'
pipeline.affymetrixQualityCheck: no visible global function definition
  for 'boxplot'
pipeline.affymetrixQualityCheck: no visible binding for global variable
  'groupwise.group.colors'
pipeline.affymetrixQualityCheck: no visible global function definition
  for 'axis'
pipeline.affymetrixQualityCheck: no visible global function definition
  for 'abline'
pipeline.affymetrixQualityCheck: no visible global function definition
  for 'plot'
pipeline.affymetrixQualityCheck: no visible global function definition
  for 'lines'
pipeline.calcStatistics: no visible binding for '<<-' assignment to
  'WAD.g.m'
pipeline.calcStatistics: no visible binding for global variable
  'indata'
pipeline.calcStatistics: no visible binding for global variable
  'WAD.g.m'
pipeline.calcStatistics: no visible binding for '<<-' assignment to
  't.g.m'
pipeline.calcStatistics: no visible binding for '<<-' assignment to
  'p.g.m'
pipeline.calcStatistics: no visible binding for '<<-' assignment to
  'n.0.m'
pipeline.calcStatistics: no visible binding for global variable 'n.0.m'
pipeline.calcStatistics: no visible binding for '<<-' assignment to
  'perc.DE.m'
pipeline.calcStatistics: no visible binding for global variable
  'perc.DE.m'
pipeline.calcStatistics: no visible binding for '<<-' assignment to
  'fdr.g.m'
pipeline.calcStatistics: no visible binding for '<<-' assignment to
  'Fdr.g.m'
pipeline.calcStatistics: no visible binding for global variable
  'indata.gene.mean'
pipeline.calcStatistics: no visible binding for global variable 'sd'
pipeline.calcStatistics: no visible binding for global variable 't.g.m'
pipeline.calcStatistics: no visible binding for global variable 'p.g.m'
pipeline.calcStatistics: no visible binding for global variable
  'fdr.g.m'
pipeline.calcStatistics: no visible binding for global variable
  'Fdr.g.m'
pipeline.calcStatistics: no visible binding for '<<-' assignment to
  't.m'
pipeline.calcStatistics: no visible binding for '<<-' assignment to
  'p.m'
pipeline.calcStatistics: no visible binding for global variable
  'preferences'
pipeline.calcStatistics: no visible binding for global variable
  'som.result'
pipeline.calcStatistics: no visible binding for global variable 't.m'
pipeline.calcStatistics: no visible global function definition for
  'na.omit'
pipeline.calcStatistics: no visible binding for global variable 'p.m'
pipeline.cancerHallmarks : <anonymous>: no visible binding for global
  variable 'gs.def.list'
pipeline.cancerHallmarks : <anonymous>: no visible binding for global
  variable 'gene.info'
pipeline.cancerHallmarks: no visible binding for global variable
  'indata'
pipeline.cancerHallmarks : <anonymous>: no visible binding for global
  variable 'unique.protein.ids'
pipeline.cancerHallmarks : <anonymous>: no visible binding for global
  variable 't.ensID.m'
pipeline.cancerHallmarks: no visible binding for global variable
  'preferences'
pipeline.cancerHallmarks : <anonymous>: no visible global function
  definition for 'na.omit'
pipeline.cancerHallmarks: no visible binding for global variable
  'files.name'
pipeline.cancerHallmarks: no visible global function definition for
  'pdf'
pipeline.cancerHallmarks: no visible global function definition for
  'layout'
pipeline.cancerHallmarks: no visible binding for global variable
  'group.labels'
pipeline.cancerHallmarks: no visible global function definition for
  'par'
pipeline.cancerHallmarks: no visible global function definition for
  'boxplot'
pipeline.cancerHallmarks: no visible binding for global variable
  'groupwise.group.colors'
pipeline.cancerHallmarks: no visible global function definition for
  'abline'
pipeline.cancerHallmarks: no visible binding for global variable
  'som.result'
pipeline.cancerHallmarks: no visible global function definition for
  'color.palette.heatmaps'
pipeline.cancerHallmarks: no visible global function definition for
  'na.omit'
pipeline.cancerHallmarks: no visible global function definition for
  'plot'
pipeline.cancerHallmarks: no visible global function definition for
  'title'
pipeline.cancerHallmarks: no visible global function definition for
  'box'
pipeline.cancerHallmarks: no visible global function definition for
  'frame'
pipeline.cancerHallmarks: no visible global function definition for
  'legend'
pipeline.cancerHallmarks: no visible global function definition for
  'dev.off'
pipeline.checkInputParameters: no visible binding for global variable
  'env'
pipeline.checkInputParameters : <anonymous>: no visible binding for
  global variable 'indata'
pipeline.checkInputParameters : <anonymous> : <anonymous>: no visible
  global function definition for 'na.omit'
pipeline.checkInputParameters: no visible binding for global variable
  'indata'
pipeline.checkInputParameters: no visible binding for '<<-' assignment
  to 'group.labels'
pipeline.checkInputParameters: no visible binding for '<<-' assignment
  to 'group.colors'
pipeline.checkInputParameters: no visible binding for '<<-' assignment
  to 'indata'
pipeline.checkInputParameters: no visible binding for global variable
  'group.labels'
pipeline.checkInputParameters: no visible binding for global variable
  'group.colors'
pipeline.checkInputParameters: no visible global function definition
  for 'colorRampPalette'
pipeline.checkInputParameters: no visible global function definition
  for 'col2rgb'
pipeline.checkInputParameters : <anonymous>: no visible global function
  definition for 'rgb'
pipeline.checkInputParameters: no visible binding for '<<-' assignment
  to 'groupwise.group.colors'
pipeline.checkInputParameters: no visible binding for global variable
  'groupwise.group.colors'
pipeline.checkInputParameters: no visible binding for global variable
  'color.palette.portraits'
pipeline.checkInputParameters: no visible binding for '<<-' assignment
  to 'color.palette.portraits'
pipeline.checkInputParameters: no visible binding for global variable
  'color.palette.heatmaps'
pipeline.checkInputParameters: no visible binding for '<<-' assignment
  to 'color.palette.heatmaps'
pipeline.checkInputParameters: no visible binding for '<<-' assignment
  to 'files.name'
pipeline.checkInputParameters: no visible binding for global variable
  'files.name'
pipeline.checkInputParameters: no visible binding for '<<-' assignment
  to 'output.paths'
pipeline.chromosomeExpressionReports: no visible binding for global
  variable 'chromosome.list'
pipeline.chromosomeExpressionReports : <anonymous>: no visible binding
  for global variable 'gene.info'
pipeline.chromosomeExpressionReports: no visible binding for global
  variable 'indata'
pipeline.chromosomeExpressionReports : <anonymous>: no visible binding
  for global variable 'indata'
pipeline.chromosomeExpressionReports: no visible global function
  definition for 'hclust'
pipeline.chromosomeExpressionReports: no visible global function
  definition for 'dist'
pipeline.chromosomeExpressionReports: no visible binding for global
  variable 'files.name'
pipeline.chromosomeExpressionReports: no visible global function
  definition for 'pdf'
pipeline.chromosomeExpressionReports: no visible global function
  definition for 'layout'
pipeline.chromosomeExpressionReports: no visible global function
  definition for 'par'
pipeline.chromosomeExpressionReports: no visible global function
  definition for 'image'
pipeline.chromosomeExpressionReports: no visible global function
  definition for 'color.palette.heatmaps'
pipeline.chromosomeExpressionReports: no visible global function
  definition for 'box'
pipeline.chromosomeExpressionReports: no visible global function
  definition for 'abline'
pipeline.chromosomeExpressionReports: no visible global function
  definition for 'axis'
pipeline.chromosomeExpressionReports: no visible binding for global
  variable 'group.colors'
pipeline.chromosomeExpressionReports: no visible global function
  definition for 'dev.off'
pipeline.detectEnsemblDataset: no visible binding for '<<-' assignment
  to 'preferences'
pipeline.detectEnsemblDataset: no visible binding for global variable
  'preferences'
pipeline.detectEnsemblDataset: no visible binding for global variable
  'indata'
pipeline.detectSpotsIntegral: no visible binding for global variable
  'metadata'
pipeline.detectSpotsIntegral: no visible binding for global variable
  'indata'
pipeline.detectSpotsIntegral: no visible binding for global variable
  'preferences'
pipeline.detectSpotsIntegral: no visible binding for '<<-' assignment
  to 'spot.list.overexpression'
pipeline.detectSpotsIntegral: no visible binding for global variable
  'spot.list.overexpression'
pipeline.detectSpotsIntegral: no visible binding for global variable
  'som.result'
pipeline.detectSpotsIntegral : <anonymous>: no visible binding for
  global variable 'metadata'
pipeline.detectSpotsIntegral : <anonymous>: no visible binding for
  global variable 'indata'
pipeline.detectSpotsIntegral: no visible binding for '<<-' assignment
  to 'spot.list.underexpression'
pipeline.detectSpotsIntegral: no visible binding for global variable
  'spot.list.underexpression'
pipeline.detectSpotsIntegral: no visible binding for '<<-' assignment
  to 'spot.list.correlation'
pipeline.detectSpotsIntegral: no visible binding for global variable
  'spot.list.correlation'
pipeline.detectSpotsIntegral: no visible global function definition for
  'cor'
pipeline.detectSpotsIntegral: no visible global function definition for
  'kmeans'
pipeline.detectSpotsIntegral: no visible binding for '<<-' assignment
  to 'spot.list.kmeans'
pipeline.detectSpotsIntegral: no visible binding for global variable
  'spot.list.kmeans'
pipeline.detectSpotsIntegral: no visible binding for global variable
  'group.labels'
pipeline.detectSpotsIntegral: no visible binding for '<<-' assignment
  to 'spot.list.group.overexpression'
pipeline.detectSpotsIntegral: no visible binding for global variable
  'spot.list.group.overexpression'
pipeline.detectSpotsIntegral : <anonymous>: no visible binding for
  global variable 'preferences'
pipeline.detectSpotsIntegral : <anonymous>: no visible global function
  definition for 'dist'
pipeline.detectSpotsIntegral: no visible binding for '<<-' assignment
  to 'spot.list.dmap'
pipeline.detectSpotsIntegral: no visible binding for global variable
  'spot.list.dmap'
pipeline.detectSpotsIntegral: no visible global function definition for
  'na.omit'
pipeline.detectSpotsIntegral : <anonymous>: no visible global function
  definition for 'sd'
pipeline.detectSpotsIntegral : <anonymous>: no visible binding for
  global variable 'spot.list.dmap'
pipeline.detectSpotsSamples: no visible binding for '<<-' assignment to
  'spot.list.samples'
pipeline.detectSpotsSamples: no visible binding for global variable
  'indata'
pipeline.detectSpotsSamples: no visible binding for global variable
  'spot.list.samples'
pipeline.differenceAnalyses: no visible global function definition for
  'combn'
pipeline.differenceAnalyses: no visible binding for global variable
  'files.name'
pipeline.differenceAnalyses: no visible binding for global variable
  'var'
pipeline.differenceAnalyses: no visible global function definition for
  'pt'
pipeline.entropyProfiles: no visible binding for global variable
  'files.name'
pipeline.entropyProfiles: no visible global function definition for
  'pdf'
pipeline.entropyProfiles: no visible global function definition for
  'par'
pipeline.entropyProfiles: no visible global function definition for
  'barplot'
pipeline.entropyProfiles: no visible binding for global variable
  'metadata'
pipeline.entropyProfiles: no visible binding for global variable
  'group.colors'
pipeline.entropyProfiles: no visible binding for global variable
  'indata'
pipeline.entropyProfiles: no visible global function definition for
  'box'
pipeline.entropyProfiles: no visible binding for global variable
  'group.labels'
pipeline.entropyProfiles: no visible global function definition for
  'boxplot'
pipeline.entropyProfiles: no visible binding for global variable
  'groupwise.group.colors'
pipeline.entropyProfiles: no visible global function definition for
  'axis'
pipeline.entropyProfiles: no visible binding for global variable 'var'
pipeline.entropyProfiles: no visible global function definition for
  'quantile'
pipeline.entropyProfiles : <anonymous>: no visible global function
  definition for 'hist'
pipeline.entropyProfiles : <anonymous>: no visible binding for global
  variable 'preferences'
pipeline.entropyProfiles: no visible binding for global variable
  'som.result'
pipeline.entropyProfiles: no visible global function definition for
  'dev.off'
pipeline.geneLists: no visible binding for global variable 'som.result'
pipeline.geneLists: no visible binding for global variable 'indata'
pipeline.geneLists: no visible binding for global variable 'gene.info'
pipeline.geneLists: no visible binding for global variable
  'indata.gene.mean'
pipeline.geneLists: no visible binding for global variable 'files.name'
pipeline.geneLists: no visible global function definition for
  'write.csv2'
pipeline.geneLists: no visible binding for global variable
  'output.paths'
pipeline.geneLists: no visible binding for global variable
  'samples.GSZ.scores'
pipeline.geneLists: no visible binding for global variable
  'preferences'
pipeline.geneLists: no visible binding for global variable 'p.g.m'
pipeline.geneLists: no visible binding for global variable 'WAD.g.m'
pipeline.geneLists: no visible binding for global variable 't.g.m'
pipeline.geneLists: no visible binding for global variable 'fdr.g.m'
pipeline.geneLists: no visible binding for global variable 'Fdr.g.m'
pipeline.geneLists: no visible binding for global variable 'perc.DE.m'
pipeline.geneLists: no visible binding for global variable
  'spot.list.samples'
pipeline.generateSOM: no visible binding for '<<-' assignment to
  'som.result'
pipeline.generateSOM: no visible binding for global variable 'indata'
pipeline.generateSOM: no visible binding for global variable
  'preferences'
pipeline.generateSOM: no visible binding for global variable
  'som.result'
pipeline.generateSOM: no visible binding for '<<-' assignment to
  'metadata'
pipeline.generateSOM: no visible binding for global variable 'metadata'
pipeline.generateSOM: no visible binding for '<<-' assignment to
  'gene.info'
pipeline.generateSOM: no visible binding for global variable
  'gene.info'
pipeline.genesetOverviews: no visible binding for global variable
  'files.name'
pipeline.genesetOverviews: no visible global function definition for
  'pdf'
pipeline.genesetOverviews: no visible binding for global variable
  'preferences'
pipeline.genesetOverviews : <anonymous>: no visible binding for global
  variable 'gs.def.list'
pipeline.genesetOverviews: no visible binding for global variable
  'gs.def.list'
pipeline.genesetOverviews: no visible binding for global variable
  'samples.GSZ.scores'
pipeline.genesetOverviews: no visible binding for global variable
  'indata'
pipeline.genesetOverviews: no visible global function definition for
  'quantile'
pipeline.genesetOverviews: no visible global function definition for
  'color.palette.heatmaps'
pipeline.genesetOverviews: no visible binding for global variable
  'group.colors'
pipeline.genesetOverviews: no visible global function definition for
  'par'
pipeline.genesetOverviews: no visible global function definition for
  'image'
pipeline.genesetOverviews: no visible global function definition for
  'box'
pipeline.genesetOverviews: no visible global function definition for
  'axis'
pipeline.genesetOverviews: no visible global function definition for
  'mtext'
pipeline.genesetOverviews: no visible binding for global variable
  'group.labels'
pipeline.genesetOverviews : <anonymous>: no visible binding for global
  variable 'group.labels'
pipeline.genesetOverviews : <anonymous>: no visible global function
  definition for 'hclust'
pipeline.genesetOverviews : <anonymous>: no visible global function
  definition for 'dist'
pipeline.genesetOverviews: no visible binding for global variable
  'spot.list.samples'
pipeline.genesetOverviews: no visible global function definition for
  'hist'
pipeline.genesetOverviews: no visible global function definition for
  'abline'
pipeline.genesetOverviews: no visible global function definition for
  'plot'
pipeline.genesetOverviews: no visible global function definition for
  'lines'
pipeline.genesetOverviews: no visible global function definition for
  'legend'
pipeline.genesetOverviews: no visible global function definition for
  'dev.off'
pipeline.genesetProfilesAndMaps: no visible binding for global variable
  'files.name'
pipeline.genesetProfilesAndMaps: no visible binding for global variable
  'samples.GSZ.scores'
pipeline.genesetProfilesAndMaps: no visible global function definition
  for 'quantile'
pipeline.genesetProfilesAndMaps: no visible global function definition
  for 'sd'
pipeline.genesetProfilesAndMaps: no visible binding for global variable
  'gs.def.list'
pipeline.genesetProfilesAndMaps: no visible global function definition
  for 'pdf'
pipeline.genesetProfilesAndMaps: no visible global function definition
  for 'layout'
pipeline.genesetProfilesAndMaps: no visible binding for global variable
  'indata'
pipeline.genesetProfilesAndMaps: no visible binding for global variable
  'gene.info'
pipeline.genesetProfilesAndMaps: no visible binding for global variable
  'sd'
pipeline.genesetProfilesAndMaps: no visible global function definition
  for 'hclust'
pipeline.genesetProfilesAndMaps: no visible global function definition
  for 'dist'
pipeline.genesetProfilesAndMaps: no visible global function definition
  for 'par'
pipeline.genesetProfilesAndMaps: no visible global function definition
  for 'barplot'
pipeline.genesetProfilesAndMaps: no visible binding for global variable
  'group.colors'
pipeline.genesetProfilesAndMaps: no visible global function definition
  for 'abline'
pipeline.genesetProfilesAndMaps: no visible global function definition
  for 'axis'
pipeline.genesetProfilesAndMaps: no visible global function definition
  for 'mtext'
pipeline.genesetProfilesAndMaps: no visible global function definition
  for 'frame'
pipeline.genesetProfilesAndMaps: no visible global function definition
  for 'legend'
pipeline.genesetProfilesAndMaps: no visible binding for global variable
  'groupwise.group.colors'
pipeline.genesetProfilesAndMaps: no visible global function definition
  for 'image'
pipeline.genesetProfilesAndMaps: no visible global function definition
  for 'box'
pipeline.genesetProfilesAndMaps: no visible global function definition
  for 'color.palette.heatmaps'
pipeline.genesetProfilesAndMaps: no visible binding for global variable
  'preferences'
pipeline.genesetProfilesAndMaps: no visible binding for global variable
  'som.result'
pipeline.genesetProfilesAndMaps: no visible global function definition
  for 'na.omit'
pipeline.genesetProfilesAndMaps: no visible global function definition
  for 'plot'
pipeline.genesetProfilesAndMaps: no visible global function definition
  for 'title'
pipeline.genesetProfilesAndMaps: no visible binding for global variable
  'group.labels'
pipeline.genesetProfilesAndMaps: no visible global function definition
  for 'boxplot'
pipeline.genesetProfilesAndMaps: no visible global function definition
  for 'dev.off'
pipeline.genesetProfilesAndMaps: no visible global function definition
  for 'write.csv2'
pipeline.genesetProfilesAndMaps: no visible global function definition
  for 'setTxtProgressBar'
pipeline.genesetStatisticIntegral : spot.fisher.p: no visible global
  function definition for 'na.omit'
pipeline.genesetStatisticIntegral : spot.fisher.p: no visible binding
  for global variable 'gene.info'
pipeline.genesetStatisticIntegral : spot.fisher.p: no visible binding
  for global variable 'unique.protein.ids'
pipeline.genesetStatisticIntegral : spot.fisher.p: no visible binding
  for global variable 'gs.def.list'
pipeline.genesetStatisticIntegral: no visible binding for '<<-'
  assignment to 'spot.list.overexpression'
pipeline.genesetStatisticIntegral: no visible binding for global
  variable 'spot.list.overexpression'
pipeline.genesetStatisticIntegral: no visible binding for '<<-'
  assignment to 'spot.list.underexpression'
pipeline.genesetStatisticIntegral: no visible binding for global
  variable 'spot.list.underexpression'
pipeline.genesetStatisticIntegral: no visible binding for global
  variable 'spot.list.correlation'
pipeline.genesetStatisticIntegral: no visible binding for '<<-'
  assignment to 'spot.list.correlation'
pipeline.genesetStatisticIntegral: no visible binding for '<<-'
  assignment to 'spot.list.kmeans'
pipeline.genesetStatisticIntegral: no visible binding for global
  variable 'spot.list.kmeans'
pipeline.genesetStatisticIntegral: no visible binding for global
  variable 'group.labels'
pipeline.genesetStatisticIntegral: no visible binding for '<<-'
  assignment to 'spot.list.group.overexpression'
pipeline.genesetStatisticIntegral: no visible binding for global
  variable 'spot.list.group.overexpression'
pipeline.genesetStatisticIntegral: no visible binding for '<<-'
  assignment to 'spot.list.dmap'
pipeline.genesetStatisticIntegral: no visible binding for global
  variable 'spot.list.dmap'
pipeline.genesetStatisticSamples: no visible binding for '<<-'
  assignment to 't.ensID.m'
pipeline.genesetStatisticSamples: no visible binding for global
  variable 't.g.m'
pipeline.genesetStatisticSamples: no visible binding for global
  variable 'indata'
pipeline.genesetStatisticSamples: no visible binding for global
  variable 'gene.info'
pipeline.genesetStatisticSamples: no visible binding for global
  variable 't.ensID.m'
pipeline.genesetStatisticSamples: no visible binding for global
  variable 'preferences'
pipeline.genesetStatisticSamples: no visible binding for global
  variable 'gs.def.list'
pipeline.genesetStatisticSamples: no visible binding for global
  variable 'unique.protein.ids'
pipeline.genesetStatisticSamples : <anonymous>: no visible binding for
  global variable 't.ensID.m'
pipeline.genesetStatisticSamples : <anonymous>: no visible binding for
  global variable 'unique.protein.ids'
pipeline.genesetStatisticSamples: no visible global function definition
  for 'ecdf'
pipeline.genesetStatisticSamples: no visible binding for '<<-'
  assignment to 'spot.list.samples'
pipeline.genesetStatisticSamples: no visible binding for global
  variable 'spot.list.samples'
pipeline.genesetStatisticSamples : <anonymous>: no visible binding for
  global variable 'spot.list.samples'
pipeline.genesetStatisticSamples : <anonymous>: no visible binding for
  global variable 'gs.def.list'
pipeline.genesetStatisticSamples : <anonymous>: no visible binding for
  global variable 'preferences'
pipeline.genesetStatisticSamples: no visible binding for '<<-'
  assignment to 'samples.GSZ.scores'
pipeline.groupAnalysis: no visible binding for global variable
  'files.name'
pipeline.groupAnalysis : <anonymous>: no visible global function
  definition for 'sd'
pipeline.groupAnalysis: no visible global function definition for 'pt'
pipeline.groupAssignment: no visible binding for global variable
  'group.labels'
pipeline.groupAssignment: no visible binding for global variable
  'pat.labels'
pipeline.groupAssignment: no visible binding for global variable
  'preferences'
pipeline.groupAssignment: no visible binding for global variable
  'indata'
pipeline.groupAssignment: no visible binding for '<<-' assignment to
  'group.labels'
pipeline.groupAssignment: no visible binding for global variable
  'files.name'
pipeline.groupAssignment: no visible global function definition for
  'pdf'
pipeline.groupAssignment: no visible global function definition for
  'barplot'
pipeline.groupAssignment: no visible global function definition for
  'box'
pipeline.groupAssignment: no visible global function definition for
  'lines'
pipeline.groupAssignment: no visible global function definition for
  'abline'
pipeline.groupAssignment: no visible global function definition for
  'dev.off'
pipeline.groupAssignment: no visible binding for '<<-' assignment to
  'pat.labels'
pipeline.groupAssignment: no visible binding for '<<-' assignment to
  'group.colors'
pipeline.groupAssignment: no visible binding for global variable
  'group.colors'
pipeline.groupAssignment: no visible global function definition for
  'colorRampPalette'
pipeline.groupAssignment: no visible binding for '<<-' assignment to
  'groupwise.group.colors'
pipeline.groupAssignment: no visible binding for global variable
  'groupwise.group.colors'
pipeline.groupAssignment: no visible binding for '<<-' assignment to
  't.g.m'
pipeline.groupAssignment: no visible binding for global variable
  't.g.m'
pipeline.groupAssignment: no visible binding for '<<-' assignment to
  'p.g.m'
pipeline.groupAssignment: no visible binding for global variable
  'p.g.m'
pipeline.groupAssignment: no visible binding for '<<-' assignment to
  'fdr.g.m'
pipeline.groupAssignment: no visible binding for global variable
  'fdr.g.m'
pipeline.groupAssignment: no visible binding for '<<-' assignment to
  'Fdr.g.m'
pipeline.groupAssignment: no visible binding for global variable
  'Fdr.g.m'
pipeline.groupAssignment: no visible binding for '<<-' assignment to
  'WAD.g.m'
pipeline.groupAssignment: no visible binding for global variable
  'WAD.g.m'
pipeline.groupAssignment: no visible binding for '<<-' assignment to
  'n.0.m'
pipeline.groupAssignment: no visible binding for global variable
  'n.0.m'
pipeline.groupAssignment: no visible binding for '<<-' assignment to
  'perc.DE.m'
pipeline.groupAssignment: no visible binding for global variable
  'perc.DE.m'
pipeline.groupAssignment: no visible binding for '<<-' assignment to
  't.m'
pipeline.groupAssignment: no visible binding for global variable 't.m'
pipeline.groupAssignment: no visible binding for '<<-' assignment to
  'p.m'
pipeline.groupAssignment: no visible binding for global variable 'p.m'
pipeline.groupAssignment: no visible binding for '<<-' assignment to
  'indata'
pipeline.groupAssignment: no visible binding for '<<-' assignment to
  'metadata'
pipeline.groupAssignment: no visible binding for global variable
  'metadata'
pipeline.groupAssignment: no visible binding for '<<-' assignment to
  'indata.sample.mean'
pipeline.groupAssignment: no visible binding for global variable
  'indata.sample.mean'
pipeline.groupAssignment: no visible binding for '<<-' assignment to
  'spot.list.samples'
pipeline.groupAssignment: no visible binding for global variable
  'spot.list.samples'
pipeline.groupAssignment: no visible binding for '<<-' assignment to
  'group.silhouette.coef'
pipeline.groupAssignment: no visible global function definition for
  'cor'
pipeline.groupAssignment : <anonymous>: no visible binding for global
  variable 'group.labels'
pipeline.groupAssignment: no visible binding for global variable
  'group.silhouette.coef'
pipeline.groupSpecificGenesets: no visible global function definition
  for 'sd'
pipeline.groupSpecificGenesets: no visible binding for global variable
  'samples.GSZ.scores'
pipeline.groupSpecificGenesets: no visible binding for global variable
  'group.labels'
pipeline.groupSpecificGenesets : <anonymous>: no visible global
  function definition for 'wilcox.test'
pipeline.groupSpecificGenesets : <anonymous>: no visible binding for
  global variable 'group.labels'
pipeline.groupSpecificGenesets: no visible global function definition
  for 'pdf'
pipeline.groupSpecificGenesets: no visible binding for global variable
  'files.name'
pipeline.groupSpecificGenesets: no visible global function definition
  for 'layout'
pipeline.groupSpecificGenesets: no visible global function definition
  for 'par'
pipeline.groupSpecificGenesets: no visible global function definition
  for 'barplot'
pipeline.groupSpecificGenesets: no visible binding for global variable
  'group.colors'
pipeline.groupSpecificGenesets: no visible binding for global variable
  'indata'
pipeline.groupSpecificGenesets: no visible global function definition
  for 'abline'
pipeline.groupSpecificGenesets: no visible global function definition
  for 'title'
pipeline.groupSpecificGenesets: no visible global function definition
  for 'mtext'
pipeline.groupSpecificGenesets: no visible binding for global variable
  'preferences'
pipeline.groupSpecificGenesets: no visible binding for global variable
  'som.result'
pipeline.groupSpecificGenesets: no visible binding for global variable
  'gene.info'
pipeline.groupSpecificGenesets: no visible binding for global variable
  'gs.def.list'
pipeline.groupSpecificGenesets: no visible global function definition
  for 'plot'
pipeline.groupSpecificGenesets: no visible global function definition
  for 'na.omit'
pipeline.groupSpecificGenesets: no visible global function definition
  for 'color.palette.heatmaps'
pipeline.groupSpecificGenesets: no visible global function definition
  for 'box'
pipeline.groupSpecificGenesets: no visible global function definition
  for 'dev.off'
pipeline.groupSpecificGenesets: no visible global function definition
  for 'write.csv2'
pipeline.groupSpecificGenesets : <anonymous>: no visible global
  function definition for 'aov'
pipeline.groupSpecificGenesets: no visible global function definition
  for 'text'
pipeline.groupSpecificGenesets: no visible binding for global variable
  'groupwise.group.colors'
pipeline.htmlDifferencesSummary: no visible binding for global variable
  'files.name'
pipeline.htmlDifferencesSummary: no visible binding for global variable
  'indata'
pipeline.htmlGenesetAnalysis: no visible binding for global variable
  'preferences'
pipeline.htmlGenesetAnalysis: no visible binding for global variable
  'files.name'
pipeline.htmlGenesetAnalysis: no visible binding for global variable
  'gs.def.list'
pipeline.htmlGroupSummary: no visible binding for global variable
  'group.labels'
pipeline.htmlGroupSummary: no visible binding for global variable
  'files.name'
pipeline.htmlGroupSummary: no visible binding for global variable
  'preferences'
pipeline.htmlGroupSummary: no visible binding for global variable
  'indata'
pipeline.htmlModuleSummary: no visible binding for global variable
  'files.name'
pipeline.htmlModuleSummary: no visible binding for global variable
  'group.labels'
pipeline.htmlModuleSummary: no visible binding for global variable
  'spot.list.overexpression'
pipeline.htmlModuleSummary: no visible binding for global variable
  'spot.list.group.overexpression'
pipeline.htmlModuleSummary: no visible binding for global variable
  'spot.list.kmeans'
pipeline.htmlModuleSummary: no visible binding for global variable
  'spot.list.dmap'
pipeline.htmlSampleSummary: no visible binding for global variable
  'indata'
pipeline.htmlSampleSummary: no visible binding for global variable
  'files.name'
pipeline.htmlSampleSummary: no visible binding for global variable
  'group.labels'
pipeline.htmlSummary: no visible binding for global variable
  'files.name'
pipeline.htmlSummary: no visible binding for global variable 'indata'
pipeline.htmlSummary: no visible binding for global variable
  'group.labels'
pipeline.htmlSummary: no visible binding for global variable
  'preferences'
pipeline.moduleCorrelationMap: no visible global function definition
  for 'quantile'
pipeline.moduleCorrelationMap: no visible global function definition
  for 'layout'
pipeline.moduleCorrelationMap: no visible global function definition
  for 'par'
pipeline.moduleCorrelationMap: no visible global function definition
  for 'image'
pipeline.moduleCorrelationMap: no visible binding for global variable
  'group.colors'
pipeline.moduleCorrelationMap: no visible global function definition
  for 'color.palette.heatmaps'
pipeline.moduleCorrelationMap: no visible global function definition
  for 'box'
pipeline.moduleCorrelationMap : <anonymous>: no visible global function
  definition for 'rect'
pipeline.moduleCorrelationMap: no visible binding for global variable
  'preferences'
pipeline.moduleCorrelationMap : <anonymous>: no visible global function
  definition for 'sd'
pipeline.moduleCorrelationMap : <anonymous>: no visible global function
  definition for 'text'
pipeline.moduleCorrelationMap: no visible global function definition
  for 'as.dendrogram'
pipeline.moduleCorrelationMap: no visible global function definition
  for 'plot'
pipeline.moduleCorrelationMap: no visible global function definition
  for 'title'
pipeline.patAssignment: no visible binding for global variable
  'preferences'
pipeline.patAssignment: no visible global function definition for 'sd'
pipeline.patAssignment: no visible binding for '<<-' assignment to
  'pat.labels'
pipeline.patAssignment: no visible binding for global variable
  'pat.labels'
pipeline.prepareAnnotation: no visible binding for global variable
  'indata'
pipeline.prepareAnnotation: no visible binding for '<<-' assignment to
  'gene.info'
pipeline.prepareAnnotation: no visible binding for '<<-' assignment to
  'chromosome.list'
pipeline.prepareAnnotation: no visible binding for '<<-' assignment to
  'preferences'
pipeline.prepareAnnotation: no visible binding for global variable
  'preferences'
pipeline.prepareAnnotation: no visible binding for global variable
  'gene.info'
pipeline.prepareAnnotation: no visible binding for global variable
  'chromosome.list'
pipeline.prepareAnnotation: no visible binding for '<<-' assignment to
  'unique.protein.ids'
pipeline.prepareAnnotation: no visible binding for global variable
  'unique.protein.ids'
pipeline.prepareAnnotation: no visible binding for '<<-' assignment to
  'gs.def.list'
pipeline.prepareAnnotation: no visible binding for global variable
  'gs.def.list'
pipeline.prepareAnnotation: no visible binding for global variable
  'head'
pipeline.prepareAnnotation : <anonymous>: no visible binding for global
  variable 'gene.info'
pipeline.prepareAnnotation: no visible global function definition for
  'data'
pipeline.prepareAnnotation: no visible binding for global variable
  'opossom.genesets'
pipeline.prepareAnnotation : <anonymous>: no visible binding for global
  variable 'unique.protein.ids'
pipeline.prepareIndata: no visible binding for '<<-' assignment to
  'indata.sample.mean'
pipeline.prepareIndata: no visible binding for global variable 'indata'
pipeline.prepareIndata: no visible binding for global variable
  'preferences'
pipeline.prepareIndata: no visible binding for '<<-' assignment to
  'indata'
pipeline.prepareIndata: no visible binding for '<<-' assignment to
  'group.labels'
pipeline.prepareIndata: no visible binding for global variable
  'group.labels'
pipeline.prepareIndata: no visible binding for '<<-' assignment to
  'group.colors'
pipeline.prepareIndata: no visible binding for global variable
  'group.colors'
pipeline.prepareIndata: no visible binding for '<<-' assignment to
  'indata.gene.mean'
pipeline.prepareIndata: no visible binding for global variable
  'indata.gene.mean'
pipeline.qualityCheck: no visible binding for global variable
  'files.name'
pipeline.qualityCheck : plot.poly.density: no visible binding for
  global variable 'indata'
pipeline.qualityCheck : plot.poly.density: no visible global function
  definition for 'par'
pipeline.qualityCheck : plot.poly.density: no visible global function
  definition for 'plot'
pipeline.qualityCheck : plot.poly.density: no visible global function
  definition for 'lines'
pipeline.qualityCheck : plot.poly.density: no visible global function
  definition for 'polygon'
pipeline.qualityCheck : plot.poly.density: no visible binding for
  global variable 'sd'
pipeline.qualityCheck: no visible binding for global variable 'indata'
pipeline.qualityCheck : <anonymous>: no visible global function
  definition for 'density'
pipeline.qualityCheck: no visible global function definition for 'pdf'
pipeline.qualityCheck: no visible global function definition for 'par'
pipeline.qualityCheck: no visible global function definition for 'plot'
pipeline.qualityCheck: no visible binding for global variable 'lines'
pipeline.qualityCheck: no visible binding for global variable
  'group.labels'
pipeline.qualityCheck: no visible binding for global variable
  'groupwise.group.colors'
pipeline.qualityCheck: no visible binding for global variable 'sd'
pipeline.qualityCheck: no visible global function definition for
  'quantile'
pipeline.qualityCheck: no visible binding for global variable
  'group.colors'
pipeline.qualityCheck: no visible global function definition for
  'abline'
pipeline.qualityCheck: no visible global function definition for
  'legend'
pipeline.qualityCheck: no visible global function definition for 'text'
pipeline.qualityCheck: no visible global function definition for
  'barplot'
pipeline.qualityCheck: no visible global function definition for 'box'
pipeline.qualityCheck: no visible global function definition for
  'boxplot'
pipeline.qualityCheck: no visible global function definition for 'axis'
pipeline.qualityCheck: no visible global function definition for
  'dev.off'
pipeline.sampleExpressionPortraits: no visible binding for global
  variable 'files.name'
pipeline.sampleExpressionPortraits: no visible global function
  definition for 'pdf'
pipeline.sampleExpressionPortraits: no visible global function
  definition for 'par'
pipeline.sampleExpressionPortraits: no visible binding for global
  variable 'group.labels'
pipeline.sampleExpressionPortraits: no visible global function
  definition for 'plot'
pipeline.sampleExpressionPortraits: no visible global function
  definition for 'mtext'
pipeline.sampleExpressionPortraits: no visible binding for global
  variable 'groupwise.group.colors'
pipeline.sampleExpressionPortraits: no visible global function
  definition for 'image'
pipeline.sampleExpressionPortraits: no visible binding for global
  variable 'metadata'
pipeline.sampleExpressionPortraits: no visible binding for global
  variable 'preferences'
pipeline.sampleExpressionPortraits: no visible global function
  definition for 'color.palette.portraits'
pipeline.sampleExpressionPortraits: no visible global function
  definition for 'title'
pipeline.sampleExpressionPortraits: no visible binding for global
  variable 'indata'
pipeline.sampleExpressionPortraits: no visible binding for global
  variable 'group.silhouette.coef'
pipeline.sampleExpressionPortraits: no visible global function
  definition for 'box'
pipeline.sampleExpressionPortraits: no visible global function
  definition for 'persp'
pipeline.sampleExpressionPortraits: no visible global function
  definition for 'dev.off'
pipeline.sampleExpressionPortraits: no visible global function
  definition for 'text'
pipeline.sampleSimilarityAnalysisCor : mixColors: no visible binding
  for global variable 'rgb'
pipeline.sampleSimilarityAnalysisCor: no visible global function
  definition for 'col2rgb'
pipeline.sampleSimilarityAnalysisCor: no visible binding for global
  variable 'groupwise.group.colors'
pipeline.sampleSimilarityAnalysisCor : <anonymous>: no visible global
  function definition for 'rgb'
pipeline.sampleSimilarityAnalysisCor: no visible binding for global
  variable 'group.colors'
pipeline.sampleSimilarityAnalysisCor: no visible binding for global
  variable 'group.silhouette.coef'
pipeline.sampleSimilarityAnalysisCor: no visible binding for global
  variable 'group.labels'
pipeline.sampleSimilarityAnalysisCor: no visible global function
  definition for 'cor'
pipeline.sampleSimilarityAnalysisCor: no visible binding for global
  variable 'preferences'
pipeline.sampleSimilarityAnalysisCor: no visible binding for global
  variable 'metadata'
pipeline.sampleSimilarityAnalysisCor: no visible binding for global
  variable 'files.name'
pipeline.sampleSimilarityAnalysisCor: no visible global function
  definition for 'pdf'
pipeline.sampleSimilarityAnalysisCor: no visible global function
  definition for 'par'
pipeline.sampleSimilarityAnalysisCor: no visible global function
  definition for 'get.edgelist'
pipeline.sampleSimilarityAnalysisCor : <anonymous>: no visible binding
  for global variable 'group.colors'
pipeline.sampleSimilarityAnalysisCor: no visible global function
  definition for 'plot'
pipeline.sampleSimilarityAnalysisCor: no visible global function
  definition for 'legend'
pipeline.sampleSimilarityAnalysisCor: no visible global function
  definition for 'box'
pipeline.sampleSimilarityAnalysisCor: no visible global function
  definition for 'dev.off'
pipeline.sampleSimilarityAnalysisCor: no visible global function
  definition for 'hclust'
pipeline.sampleSimilarityAnalysisCor: no visible global function
  definition for 'dist'
pipeline.sampleSimilarityAnalysisCor: no visible global function
  definition for 'color.palette.heatmaps'
pipeline.sampleSimilarityAnalysisCor: no visible global function
  definition for 'image'
pipeline.sampleSimilarityAnalysisCor: no visible global function
  definition for 'axis'
pipeline.sampleSimilarityAnalysisCor : <anonymous>: no visible binding
  for global variable 'group.labels'
pipeline.sampleSimilarityAnalysisCor : <anonymous>: no visible global
  function definition for 'hclust'
pipeline.sampleSimilarityAnalysisCor : <anonymous>: no visible global
  function definition for 'dist'
pipeline.sampleSimilarityAnalysisCor: no visible global function
  definition for 'as.dendrogram'
pipeline.sampleSimilarityAnalysisED: no visible binding for global
  variable 'files.name'
pipeline.sampleSimilarityAnalysisED: no visible global function
  definition for 'pdf'
pipeline.sampleSimilarityAnalysisED: no visible binding for global
  variable 'preferences'
pipeline.sampleSimilarityAnalysisED: no visible binding for global
  variable 'metadata'
pipeline.sampleSimilarityAnalysisED: no visible global function
  definition for 'par'
pipeline.sampleSimilarityAnalysisED: no visible global function
  definition for 'plot'
pipeline.sampleSimilarityAnalysisED: no visible binding for global
  variable 'group.colors'
pipeline.sampleSimilarityAnalysisED: no visible global function
  definition for 'title'
pipeline.sampleSimilarityAnalysisED: no visible global function
  definition for 'legend'
pipeline.sampleSimilarityAnalysisED: no visible binding for global
  variable 'group.labels'
pipeline.sampleSimilarityAnalysisED: no visible binding for global
  variable 'groupwise.group.colors'
pipeline.sampleSimilarityAnalysisED: no visible global function
  definition for 'dev.off'
pipeline.sampleSimilarityAnalysisED: no visible global function
  definition for 'dist'
pipeline.sampleSimilarityAnalysisED: no visible global function
  definition for 'box'
pipeline.sampleSimilarityAnalysisED: no visible global function
  definition for 'color.palette.heatmaps'
pipeline.sampleSimilarityAnalysisED: no visible global function
  definition for 'image'
pipeline.sampleSimilarityAnalysisED: no visible global function
  definition for 'axis'
pipeline.sampleSimilarityAnalysisICA: no visible binding for global
  variable 'files.name'
pipeline.sampleSimilarityAnalysisICA: no visible global function
  definition for 'pdf'
pipeline.sampleSimilarityAnalysisICA: no visible binding for global
  variable 'preferences'
pipeline.sampleSimilarityAnalysisICA: no visible binding for global
  variable 'metadata'
pipeline.sampleSimilarityAnalysisICA: no visible global function
  definition for 'layout'
pipeline.sampleSimilarityAnalysisICA: no visible global function
  definition for 'par'
pipeline.sampleSimilarityAnalysisICA: no visible binding for global
  variable 'group.colors'
pipeline.sampleSimilarityAnalysisICA: no visible global function
  definition for 'plot'
pipeline.sampleSimilarityAnalysisICA: no visible global function
  definition for 'text'
pipeline.sampleSimilarityAnalysisICA: no visible global function
  definition for 'mtext'
pipeline.sampleSimilarityAnalysisICA: no visible global function
  definition for 'legend'
pipeline.sampleSimilarityAnalysisICA: no visible binding for global
  variable 'group.labels'
pipeline.sampleSimilarityAnalysisICA: no visible binding for global
  variable 'groupwise.group.colors'
pipeline.sampleSimilarityAnalysisICA: no visible global function
  definition for 'points'
pipeline.sampleSimilarityAnalysisICA: no visible global function
  definition for 'box'
pipeline.sampleSimilarityAnalysisICA: no visible binding for global
  variable 'indata'
pipeline.sampleSimilarityAnalysisICA: no visible global function
  definition for 'dev.off'
pipeline.sampleSimilarityAnalysisSOM: no visible binding for global
  variable 'files.name'
pipeline.sampleSimilarityAnalysisSOM: no visible global function
  definition for 'pdf'
pipeline.sampleSimilarityAnalysisSOM: no visible binding for global
  variable 'preferences'
pipeline.sampleSimilarityAnalysisSOM: no visible binding for global
  variable 'metadata'
pipeline.sampleSimilarityAnalysisSOM: no visible global function
  definition for 'par'
pipeline.sampleSimilarityAnalysisSOM: no visible global function
  definition for 'plot'
pipeline.sampleSimilarityAnalysisSOM: no visible binding for global
  variable 'group.labels'
pipeline.sampleSimilarityAnalysisSOM: no visible global function
  definition for 'legend'
pipeline.sampleSimilarityAnalysisSOM: no visible binding for global
  variable 'groupwise.group.colors'
pipeline.sampleSimilarityAnalysisSOM: no visible global function
  definition for 'points'
pipeline.sampleSimilarityAnalysisSOM: no visible binding for global
  variable 'group.colors'
pipeline.sampleSimilarityAnalysisSOM: no visible global function
  definition for 'box'
pipeline.sampleSimilarityAnalysisSOM: no visible global function
  definition for 'text'
pipeline.sampleSimilarityAnalysisSOM: no visible binding for global
  variable 'indata'
pipeline.sampleSimilarityAnalysisSOM: no visible global function
  definition for 'chull'
pipeline.sampleSimilarityAnalysisSOM: no visible global function
  definition for 'polygon'
pipeline.sampleSimilarityAnalysisSOM: no visible global function
  definition for 'color.palette.portraits'
pipeline.sampleSimilarityAnalysisSOM: no visible global function
  definition for 'dev.off'
pipeline.summarySheetsGroups: no visible binding for global variable
  'metadata'
pipeline.summarySheetsGroups: no visible binding for global variable
  'group.labels'
pipeline.summarySheetsGroups : <anonymous>: no visible binding for
  global variable 'sd'
pipeline.summarySheetsGroups: no visible binding for global variable
  'files.name'
pipeline.summarySheetsGroups: no visible global function definition for
  'pdf'
pipeline.summarySheetsGroups: no visible global function definition for
  'par'
pipeline.summarySheetsGroups: no visible global function definition for
  'plot'
pipeline.summarySheetsGroups: no visible global function definition for
  'mtext'
pipeline.summarySheetsGroups: no visible binding for global variable
  'groupwise.group.colors'
pipeline.summarySheetsGroups: no visible global function definition for
  'image'
pipeline.summarySheetsGroups: no visible binding for global variable
  'preferences'
pipeline.summarySheetsGroups: no visible global function definition for
  'color.palette.portraits'
pipeline.summarySheetsGroups: no visible global function definition for
  'title'
pipeline.summarySheetsGroups: no visible global function definition for
  'box'
pipeline.summarySheetsGroups: no visible global function definition for
  'layout'
pipeline.summarySheetsGroups: no visible global function definition for
  'text'
pipeline.summarySheetsGroups: no visible global function definition for
  'colorRampPalette'
pipeline.summarySheetsGroups: no visible global function definition for
  'axis'
pipeline.summarySheetsGroups: no visible global function definition for
  'ecdf'
pipeline.summarySheetsGroups: no visible global function definition for
  'dev.off'
pipeline.summarySheetsGroups: no visible binding for global variable
  'group.silhouette.coef'
pipeline.summarySheetsGroups: no visible global function definition for
  'cor'
pipeline.summarySheetsGroups : <anonymous>: no visible binding for
  global variable 'group.labels'
pipeline.summarySheetsGroups: no visible binding for global variable
  'indata'
pipeline.summarySheetsGroups: no visible global function definition for
  'barplot'
pipeline.summarySheetsGroups: no visible binding for global variable
  'group.colors'
pipeline.summarySheetsGroups: no visible global function definition for
  'abline'
pipeline.summarySheetsGroups: no visible global function definition for
  'points'
pipeline.summarySheetsGroups: no visible global function definition for
  'boxplot'
pipeline.summarySheetsGroups : <anonymous>: no visible global function
  definition for 'axis'
pipeline.summarySheetsGroups : <anonymous>: no visible binding for
  global variable 'groupwise.group.colors'
pipeline.summarySheetsGroups: no visible global function definition for
  'hclust'
pipeline.summarySheetsGroups: no visible global function definition for
  'dist'
pipeline.summarySheetsGroups: no visible global function definition for
  'cutree'
pipeline.summarySheetsGroups: no visible global function definition for
  'quantile'
pipeline.summarySheetsGroups: no visible global function definition for
  'rect'
pipeline.summarySheetsModules: no visible binding for global variable
  'files.name'
pipeline.summarySheetsModules: no visible binding for global variable
  'spot.list.overexpression'
pipeline.summarySheetsModules: no visible binding for global variable
  'spot.list.underexpression'
pipeline.summarySheetsModules: no visible binding for global variable
  'spot.list.correlation'
pipeline.summarySheetsModules: no visible binding for global variable
  'spot.list.kmeans'
pipeline.summarySheetsModules: no visible binding for global variable
  'spot.list.dmap'
pipeline.summarySheetsModules: no visible binding for global variable
  'group.labels'
pipeline.summarySheetsModules: no visible binding for global variable
  'spot.list.group.overexpression'
pipeline.summarySheetsModules: no visible binding for global variable
  'output.paths'
pipeline.summarySheetsPATs: no visible binding for global variable
  'files.name'
pipeline.summarySheetsPATs: no visible binding for global variable
  'metadata'
pipeline.summarySheetsPATs: no visible binding for global variable
  'pat.labels'
pipeline.summarySheetsPATs: no visible global function definition for
  'pdf'
pipeline.summarySheetsPATs: no visible global function definition for
  'hclust'
pipeline.summarySheetsPATs: no visible global function definition for
  'dist'
pipeline.summarySheetsPATs: no visible global function definition for
  'par'
pipeline.summarySheetsPATs: no visible global function definition for
  'plot'
pipeline.summarySheetsPATs: no visible global function definition for
  'frame'
pipeline.summarySheetsPATs: no visible binding for global variable
  'preferences'
pipeline.summarySheetsPATs: no visible global function definition for
  'color.palette.portraits'
pipeline.summarySheetsPATs: no visible global function definition for
  'layout'
pipeline.summarySheetsPATs: no visible global function definition for
  'text'
pipeline.summarySheetsPATs: no visible global function definition for
  'image'
pipeline.summarySheetsPATs: no visible global function definition for
  'box'
pipeline.summarySheetsPATs: no visible binding for global variable
  'group.labels'
pipeline.summarySheetsPATs: no visible global function definition for
  'pie'
pipeline.summarySheetsPATs: no visible binding for global variable
  'groupwise.group.colors'
pipeline.summarySheetsPATs: no visible global function definition for
  'mtext'
pipeline.summarySheetsPATs : <anonymous>: no visible binding for global
  variable 'group.labels'
pipeline.summarySheetsPATs: no visible global function definition for
  'barplot'
pipeline.summarySheetsPATs: no visible global function definition for
  'legend'
pipeline.summarySheetsPATs : <anonymous>: no visible binding for global
  variable 'pat.labels'
pipeline.summarySheetsPATs: no visible global function definition for
  'dev.off'
pipeline.summarySheetsSamples: no visible binding for global variable
  'indata'
pipeline.summarySheetsSamples: no visible binding for global variable
  'output.paths'
pipeline.summarySheetsSamples: no visible binding for global variable
  'preferences'
pipeline.summarySheetsSamples: no visible binding for global variable
  'gs.def.list'
pipeline.summarySheetsSamples: no visible binding for global variable
  'gene.info'
pipeline.summarySheetsSamples: no visible global function definition
  for 'hist'
pipeline.summarySheetsSamples: no visible binding for global variable
  'p.g.m'
pipeline.summarySheetsSamples: no visible global function definition
  for 'pdf'
pipeline.summarySheetsSamples: no visible global function definition
  for 'layout'
pipeline.summarySheetsSamples: no visible global function definition
  for 'par'
pipeline.summarySheetsSamples: no visible global function definition
  for 'plot'
pipeline.summarySheetsSamples: no visible global function definition
  for 'text'
pipeline.summarySheetsSamples: no visible binding for global variable
  'perc.DE.m'
pipeline.summarySheetsSamples: no visible binding for global variable
  'fdr.g.m'
pipeline.summarySheetsSamples: no visible binding for global variable
  't.g.m'
pipeline.summarySheetsSamples: no visible global function definition
  for 'image'
pipeline.summarySheetsSamples: no visible binding for global variable
  'metadata'
pipeline.summarySheetsSamples: no visible global function definition
  for 'color.palette.portraits'
pipeline.summarySheetsSamples: no visible global function definition
  for 'axis'
pipeline.summarySheetsSamples: no visible global function definition
  for 'box'
pipeline.summarySheetsSamples: no visible global function definition
  for 'rect'
pipeline.summarySheetsSamples: no visible global function definition
  for 'mtext'
pipeline.summarySheetsSamples: no visible global function definition
  for 'abline'
pipeline.summarySheetsSamples: no visible binding for global variable
  'n.0.m'
pipeline.summarySheetsSamples: no visible global function definition
  for 'lines'
pipeline.summarySheetsSamples: no visible binding for global variable
  'Fdr.g.m'
pipeline.summarySheetsSamples: no visible global function definition
  for 'legend'
pipeline.summarySheetsSamples: no visible binding for global variable
  'spot.list.samples'
pipeline.summarySheetsSamples: no visible global function definition
  for 'dev.off'
pipeline.supportingMaps: no visible binding for global variable
  'files.name'
pipeline.supportingMaps: no visible global function definition for
  'pdf'
pipeline.supportingMaps: no visible global function definition for
  'par'
pipeline.supportingMaps: no visible binding for global variable
  'som.result'
pipeline.supportingMaps: no visible global function definition for
  'image'
pipeline.supportingMaps: no visible binding for global variable
  'preferences'
pipeline.supportingMaps: no visible global function definition for
  'color.palette.heatmaps'
pipeline.supportingMaps: no visible global function definition for
  'mtext'
pipeline.supportingMaps: no visible global function definition for
  'box'
pipeline.supportingMaps: no visible global function definition for
  'layout'
pipeline.supportingMaps: no visible global function definition for
  'axis'
pipeline.supportingMaps: no visible binding for global variable
  'metadata'
pipeline.supportingMaps: no visible binding for global variable 'var'
pipeline.supportingMaps: no visible binding for global variable 'p.m'
pipeline.supportingMaps: no visible global function definition for
  'colorRampPalette'
pipeline.supportingMaps: no visible global function definition for
  'quantile'
pipeline.supportingMaps : <anonymous>: no visible global function
  definition for 'hist'
pipeline.supportingMaps : <anonymous>: no visible binding for global
  variable 'indata'
pipeline.supportingMaps: no visible global function definition for
  'cor'
pipeline.supportingMaps: no visible binding for global variable
  'indata'
pipeline.supportingMaps : <anonymous>: no visible binding for global
  variable 'metadata'
pipeline.supportingMaps : <anonymous>: no visible binding for global
  variable 'preferences'
pipeline.supportingMaps: no visible global function definition for
  'dev.off'
pipeline.topologyProfiles: no visible binding for global variable
  'metadata'
pipeline.topologyProfiles: no visible binding for global variable
  'files.name'
pipeline.topologyProfiles: no visible binding for global variable
  'group.labels'
pipeline.topologyProfiles: no visible global function definition for
  'pdf'
pipeline.topologyProfiles: no visible global function definition for
  'par'
pipeline.topologyProfiles: no visible binding for global variable
  'preferences'
pipeline.topologyProfiles: no visible global function definition for
  'sd'
pipeline.topologyProfiles: no visible global function definition for
  'barplot'
pipeline.topologyProfiles: no visible binding for global variable
  'group.colors'
pipeline.topologyProfiles: no visible binding for global variable
  'indata'
pipeline.topologyProfiles: no visible global function definition for
  'box'
pipeline.topologyProfiles: no visible global function definition for
  'boxplot'
pipeline.topologyProfiles: no visible binding for global variable
  'groupwise.group.colors'
pipeline.topologyProfiles: no visible global function definition for
  'axis'
pipeline.topologyProfiles : <anonymous>: no visible binding for global
  variable 'group.labels'
pipeline.topologyProfiles : <anonymous>: no visible binding for global
  variable 'preferences'
pipeline.topologyProfiles: no visible global function definition for
  'dev.off'
radarchart: no visible global function definition for 'plot'
radarchart: no visible global function definition for 'polygon'
radarchart: no visible global function definition for 'text'
radarchart: no visible global function definition for 'arrows'
radarchart: no visible global function definition for 'points'
som.linear.init.subdata: no visible global function definition for
  'prcomp'
som.training.phase: no visible global function definition for
  'setTxtProgressBar'
util.cat: no visible global function definition for 'flush.console'
Undefined global functions or variables:
  Fdr.g.m WAD.g.m abline add_edges aov arrows as.dendrogram axis
  barplot box boxplot chromosome.list chull col2rgb
  color.palette.heatmaps color.palette.portraits colorRampPalette combn
  cor cutree data density dev.off dist ecdf env fdr.g.m files.name
  fisher.test flush.console frame gene.info get.edgelist graph.empty
  group.colors group.labels group.silhouette.coef
  groupwise.group.colors gs.def.list hclust head hist image indata
  indata.gene.mean indata.sample.mean kmeans layout legend lines
  metadata modifyList mtext n.0.m na.omit opossom.genesets
  order.dendrogram output.paths p.g.m p.m par pat.labels pbeta pdf
  perc.DE.m persp pie plot points polygon prcomp preferences pt
  quantile rect reorder rgb samples.GSZ.scores sd sessionInfo
  setTxtProgressBar som.result spot.list.correlation spot.list.dmap
  spot.list.group.overexpression spot.list.kmeans
  spot.list.overexpression spot.list.samples spot.list.underexpression
  t.ensID.m t.g.m t.m text title unique.protein.ids v var wilcox.test
  write.csv2
Consider adding
  importFrom("grDevices", "chull", "col2rgb", "colorRampPalette",
             "dev.off", "pdf", "rgb")
  importFrom("graphics", "abline", "arrows", "axis", "barplot", "box",
             "boxplot", "frame", "hist", "image", "layout", "legend",
             "lines", "mtext", "par", "persp", "pie", "plot", "points",
             "polygon", "rect", "text", "title")
  importFrom("stats", "aov", "as.dendrogram", "cor", "cutree", "density",
             "dist", "ecdf", "fisher.test", "hclust", "kmeans",
             "na.omit", "order.dendrogram", "pbeta", "prcomp", "pt",
             "quantile", "reorder", "sd", "var", "wilcox.test")
  importFrom("utils", "combn", "data", "flush.console", "head",
             "modifyList", "sessionInfo", "setTxtProgressBar",
             "write.csv2")
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 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. See section 'Writing portable packages' in
the 'Writing R Extensions' manual.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... 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-3.8-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)

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 or elapsed time > 5s
                 user system elapsed
oposSOM-package 58.72   3.83   87.45
opossom.run     18.89   1.20  122.41
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
oposSOM-package 67.13   3.68  116.64
opossom.run     21.97   1.74 1097.47
* 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: 1 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/oposSOM.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/oposSOM_2.0.0.tar.gz && rm -rf oposSOM.buildbin-libdir && mkdir oposSOM.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=oposSOM.buildbin-libdir oposSOM_2.0.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL oposSOM_2.0.0.zip && rm oposSOM_2.0.0.tar.gz oposSOM_2.0.0.zip
###
##############################################################################
##############################################################################


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install for i386

* installing *source* package 'oposSOM' ...
** libs
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mtune=generic -c DeltaMatrix.cpp -o DeltaMatrix.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mtune=generic -c DistanceCalculator.cpp -o DistanceCalculator.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mtune=generic -c NeighborhoodMatrix.cpp -o NeighborhoodMatrix.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o oposSOM.dll tmp.def DeltaMatrix.o DistanceCalculator.o NeighborhoodMatrix.o RcppExports.o -LC:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/lib/i386 -ltbb -ltbbmalloc -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/oposSOM.buildbin-libdir/oposSOM/libs/i386
** 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
In R CMD INSTALL

install for x64

* installing *source* package 'oposSOM' ...
** libs
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mtune=generic -c DeltaMatrix.cpp -o DeltaMatrix.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mtune=generic -c DistanceCalculator.cpp -o DistanceCalculator.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mtune=generic -c NeighborhoodMatrix.cpp -o NeighborhoodMatrix.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o oposSOM.dll tmp.def DeltaMatrix.o DistanceCalculator.o NeighborhoodMatrix.o RcppExports.o -LC:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/oposSOM.buildbin-libdir/oposSOM/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'oposSOM' as oposSOM_2.0.0.zip
* DONE (oposSOM)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'oposSOM' successfully unpacked and MD5 sums checked
In R CMD INSTALL