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CHECK report for oposSOM on malbec1

This page was generated on 2018-04-12 13:12:22 -0400 (Thu, 12 Apr 2018).

Package 980/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
oposSOM 1.16.0
Henry Loeffler-Wirth
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/oposSOM
Branch: RELEASE_3_6
Last Commit: 17b5341
Last Changed Date: 2017-10-30 12:40:18 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: oposSOM
Version: 1.16.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings oposSOM_1.16.0.tar.gz
StartedAt: 2018-04-12 01:35:35 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 01:38:50 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 194.9 seconds
RetCode: 0
Status:  OK 
CheckDir: oposSOM.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings oposSOM_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/oposSOM.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘oposSOM/DESCRIPTION’ ... OK
* this is package ‘oposSOM’ version ‘1.16.0’
* 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 loading without being on the library search path ... 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: no visible global function definition for ‘as’
modules.relations: no visible binding for global variable
  ‘group.labels’
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 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’
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
  ‘samples.GSZ.scores’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
  ‘files.name’
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.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: 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 ‘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’
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 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 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
  preferences pt quantile rect reorder rgb samples.GSZ.scores sd
  sessionInfo 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("methods", "as")
  importFrom("stats", "aov", "as.dendrogram", "cor", "cutree", "density",
             "dist", "ecdf", "fisher.test", "hclust", "kmeans",
             "na.omit", "order.dendrogram", "pbeta", "pt", "quantile",
             "reorder", "sd", "var", "wilcox.test")
  importFrom("utils", "combn", "data", "flush.console", "head",
             "modifyList", "sessionInfo", "write.csv2")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
oposSOM-package 25.504  0.264  52.155
opossom.run      9.076  0.228  31.433
* 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 NOTE
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/oposSOM.Rcheck/00check.log’
for details.



Installation output

oposSOM.Rcheck/00install.out

* installing *source* package ‘oposSOM’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (oposSOM)

Tests output


Example timings

oposSOM.Rcheck/oposSOM-Ex.timings

nameusersystemelapsed
oposSOM-package25.504 0.26452.155
opossom.new0.1760.0000.177
opossom.run 9.076 0.22831.433