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CHECK report for oposSOM on celaya2

This page was generated on 2019-10-16 12:53:29 -0400 (Wed, 16 Oct 2019).

Package 1146/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
oposSOM 2.2.0
Henry Loeffler-Wirth
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/oposSOM
Branch: RELEASE_3_9
Last Commit: a3bf5b4
Last Changed Date: 2019-05-02 11:53:48 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: oposSOM
Version: 2.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:oposSOM.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings oposSOM_2.2.0.tar.gz
StartedAt: 2019-10-16 05:16:46 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 05:21:04 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 258.3 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: oposSOM.Rcheck
Warnings: 3

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:oposSOM.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings oposSOM_2.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/oposSOM.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘oposSOM/DESCRIPTION’ ... OK
* this is package ‘oposSOM’ version ‘2.2.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘oposSOM’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* 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
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:
  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
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 : : 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 : : no visible binding for global
  variable ‘indata’
modules.CSV.sheets : : 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 : : 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 : : no visible binding for global variable
  ‘group.labels’
modules.relations :  : : no visible binding for
  global variable ‘group.labels’
modules.relations :  : : 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 : : 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 : : no visible binding for global
  variable ‘indata’
modules.report.sheets : : 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 : : 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 binding for global variable ‘write.csv2’
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 : : no visible binding for global
  variable ‘gs.def.list’
pipeline.cancerHallmarks : : no visible binding for global
  variable ‘gene.info’
pipeline.cancerHallmarks: no visible binding for global variable
  ‘indata’
pipeline.cancerHallmarks : : no visible binding for global
  variable ‘unique.protein.ids’
pipeline.cancerHallmarks : : no visible binding for global
  variable ‘t.ensID.m’
pipeline.cancerHallmarks: no visible binding for global variable
  ‘preferences’
pipeline.cancerHallmarks : : 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 : : no visible binding for
  global variable ‘indata’
pipeline.checkInputParameters :  : : 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 : : 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.checkInputParameters: no visible global function definition
  for ‘sessionInfo’
pipeline.checkInputParameters: no visible binding for '<<-' assignment
  to ‘write.csv2’
pipeline.checkInputParameters: no visible binding for global variable
  ‘write.csv’
pipeline.chromosomeExpressionReports: no visible binding for global
  variable ‘chromosome.list’
pipeline.chromosomeExpressionReports : : no visible binding
  for global variable ‘gene.info’
pipeline.chromosomeExpressionReports: no visible binding for global
  variable ‘indata’
pipeline.chromosomeExpressionReports : : 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 : : no visible binding for
  global variable ‘metadata’
pipeline.detectSpotsIntegral : : 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 : : no visible binding for
  global variable ‘preferences’
pipeline.detectSpotsIntegral : : 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 : : no visible global function
  definition for ‘sd’
pipeline.detectSpotsIntegral : : no visible binding for
  global variable ‘spot.list.dmap’
pipeline.detectSpotsIntegral: no visible binding for '<<-' assignment
  to ‘preferences’
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 : : no visible global function
  definition for ‘hist’
pipeline.entropyProfiles : : 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 : : 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 : : no visible binding for global
  variable ‘group.labels’
pipeline.genesetOverviews : : no visible global function
  definition for ‘hclust’
pipeline.genesetOverviews : : 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 : : no visible binding for
  global variable ‘t.ensID.m’
pipeline.genesetStatisticSamples : : 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 : : no visible binding for
  global variable ‘spot.list.samples’
pipeline.genesetStatisticSamples : : no visible binding for
  global variable ‘gs.def.list’
pipeline.genesetStatisticSamples : : 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 : : 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 : : 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 : : no visible global
  function definition for ‘wilcox.test’
pipeline.groupSpecificGenesets : : 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 : : 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 : : no visible global function
  definition for ‘rect’
pipeline.moduleCorrelationMap: no visible binding for global variable
  ‘preferences’
pipeline.moduleCorrelationMap : : no visible global function
  definition for ‘sd’
pipeline.moduleCorrelationMap : : 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 : : 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 : : 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 : : 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 : : 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 : : 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 : : no visible binding
  for global variable ‘group.labels’
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 ‘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 : : 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 : : 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 : : no visible global function
  definition for ‘axis’
pipeline.summarySheetsGroups : : 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 : : 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 : : 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 binding for global variable
  ‘som.result’
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 : : no visible global function
  definition for ‘hist’
pipeline.supportingMaps : : 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 : : no visible binding for global
  variable ‘metadata’
pipeline.supportingMaps : : 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 : : no visible binding for global
  variable ‘group.labels’
pipeline.topologyProfiles : : 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.csv 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.csv", "write.csv2")
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.GSZ’ ‘GeneSet.maxmean’
  ‘Get.Running.Average’ ‘Quantile.Normalization’ ‘Smooth.Matrix’
  ‘_oposSOM_calculateDelta’ ‘_oposSOM_calculateEuclideanDistances’
  ‘_oposSOM_calculateNeighborhoodMatrix’
  ‘_oposSOM_matrixToCodebookMatrix’ ‘biomart.available’
  ‘calculateDelta’ ‘calculateEuclideanDistances’
  ‘calculateNeighborhoodMatrix’ ‘col.pix’ ‘get.beta.statistic’
  ‘get.neighbors’ ‘heatmap’ ‘heatmap.A4’ ‘matrixToCodebookMatrix’
  ‘modules.CSV.sheets’ ‘modules.chromosomes’ ‘modules.profiles’
  ‘modules.relations’ ‘modules.report.sheets’ ‘newProgressBar’
  ‘pipeline.affymetrixQualityCheck’ ‘pipeline.calcStatistics’
  ‘pipeline.cancerHallmarks’ ‘pipeline.checkInputParameters’
  ‘pipeline.chromosomeExpressionReports’
  ‘pipeline.detectEnsemblDataset’ ‘pipeline.detectSpotsIntegral’
  ‘pipeline.detectSpotsSamples’ ‘pipeline.differenceAnalyses’
  ‘pipeline.entropyProfiles’ ‘pipeline.geneLists’
  ‘pipeline.generateSOM’ ‘pipeline.genesetOverviews’
  ‘pipeline.genesetProfilesAndMaps’ ‘pipeline.genesetStatisticIntegral’
  ‘pipeline.genesetStatisticSamples’ ‘pipeline.groupAnalysis’
  ‘pipeline.groupAssignment’ ‘pipeline.groupSpecificGenesets’
  ‘pipeline.htmlDifferencesSummary’ ‘pipeline.htmlGenesetAnalysis’
  ‘pipeline.htmlGroupSummary’ ‘pipeline.htmlModuleSummary’
  ‘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’ ‘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’
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 compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
oposSOM-package 39.333 11.152  58.901
opossom.run     18.117  2.607  38.196
* 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, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/oposSOM.Rcheck/00check.log’
for details.

Installation output

oposSOM.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL oposSOM
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘oposSOM’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppParallel/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c DeltaMatrix.cpp -o DeltaMatrix.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppParallel/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c DistanceCalculator.cpp -o DistanceCalculator.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppParallel/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c NeighborhoodMatrix.cpp -o NeighborhoodMatrix.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppParallel/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o oposSOM.so DeltaMatrix.o DistanceCalculator.o NeighborhoodMatrix.o RcppExports.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-oposSOM/00new/oposSOM/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (oposSOM)

Tests output

Example timings

oposSOM.Rcheck/oposSOM-Ex.timings

nameusersystemelapsed
oposSOM-package39.33311.15258.901
opossom.new0.2110.0040.226
opossom.run18.117 2.60738.196