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BioC 3.4: CHECK report for oposSOM on zin1

This page was generated on 2016-09-21 03:39:04 -0700 (Wed, 21 Sep 2016).

Package 849/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
oposSOM 1.11.0
Henry Loeffler-Wirth
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oposSOM
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: oposSOM
Version: 1.11.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings oposSOM_1.11.0.tar.gz
StartedAt: 2016-09-20 10:12:19 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 10:14:48 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 149.1 seconds
RetCode: 0
Status:  OK 
CheckDir: oposSOM.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings oposSOM_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/oposSOM.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.11.0’
* 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 ... NOTE
Unexported object imported by a ':::' call: ‘grDevices:::.smoothScatterCalcDensity’
  See the note in ?`:::` about the use of this operator.
* 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’
GeneSet.Fisher: no visible global function definition for ‘parSapply’
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 ‘frame’
heatmap: no visible global function definition for ‘title’
opossom.new: no visible global function definition for ‘modifyList’
opossom.run: no visible global function definition for ‘sessionInfo’
pipeline.2ndLvlComponentAnalysis: no visible binding for global
  variable ‘files.name’
pipeline.2ndLvlComponentAnalysis: no visible global function definition
  for ‘pdf’
pipeline.2ndLvlComponentAnalysis: no visible binding for global
  variable ‘metagene.filter.list’
pipeline.2ndLvlComponentAnalysis: no visible binding for global
  variable ‘metadata’
pipeline.2ndLvlComponentAnalysis: no visible global function definition
  for ‘layout’
pipeline.2ndLvlComponentAnalysis: no visible global function definition
  for ‘par’
pipeline.2ndLvlComponentAnalysis: no visible binding for global
  variable ‘group.colors’
pipeline.2ndLvlComponentAnalysis: no visible global function definition
  for ‘text’
pipeline.2ndLvlComponentAnalysis: no visible global function definition
  for ‘mtext’
pipeline.2ndLvlComponentAnalysis: no visible global function definition
  for ‘legend’
pipeline.2ndLvlComponentAnalysis: no visible binding for global
  variable ‘group.labels’
pipeline.2ndLvlComponentAnalysis: no visible binding for global
  variable ‘groupwise.group.colors’
pipeline.2ndLvlComponentAnalysis: no visible global function definition
  for ‘points’
pipeline.2ndLvlComponentAnalysis: no visible global function definition
  for ‘box’
pipeline.2ndLvlComponentAnalysis: no visible binding for global
  variable ‘indata’
pipeline.2ndLvlComponentAnalysis: no visible global function definition
  for ‘dev.off’
pipeline.2ndLvlCorrelationAnalysis: no visible global function
  definition for ‘col2rgb’
pipeline.2ndLvlCorrelationAnalysis: no visible binding for global
  variable ‘groupwise.group.colors’
pipeline.2ndLvlCorrelationAnalysis : <anonymous>: no visible global
  function definition for ‘rgb’
pipeline.2ndLvlCorrelationAnalysis: no visible binding for global
  variable ‘group.colors’
pipeline.2ndLvlCorrelationAnalysis: no visible binding for global
  variable ‘group.silhouette.coef’
pipeline.2ndLvlCorrelationAnalysis: no visible binding for global
  variable ‘group.labels’
pipeline.2ndLvlCorrelationAnalysis: no visible binding for global
  variable ‘files.name’
pipeline.2ndLvlCorrelationAnalysis: no visible global function
  definition for ‘pdf’
pipeline.2ndLvlCorrelationAnalysis: no visible binding for global
  variable ‘metagene.filter.list’
pipeline.2ndLvlCorrelationAnalysis: no visible binding for global
  variable ‘metadata’
pipeline.2ndLvlCorrelationAnalysis: no visible global function
  definition for ‘cor’
pipeline.2ndLvlCorrelationAnalysis: no visible global function
  definition for ‘par’
pipeline.2ndLvlCorrelationAnalysis: no visible binding for global
  variable ‘indata’
pipeline.2ndLvlCorrelationAnalysis: no visible global function
  definition for ‘legend’
pipeline.2ndLvlCorrelationAnalysis: no visible global function
  definition for ‘box’
pipeline.2ndLvlCorrelationAnalysis: no visible global function
  definition for ‘hclust’
pipeline.2ndLvlCorrelationAnalysis: no visible global function
  definition for ‘dist’
pipeline.2ndLvlCorrelationAnalysis: no visible global function
  definition for ‘as.dendrogram’
pipeline.2ndLvlCorrelationAnalysis: no visible global function
  definition for ‘color.palette.heatmaps’
pipeline.2ndLvlCorrelationAnalysis: no visible global function
  definition for ‘image’
pipeline.2ndLvlCorrelationAnalysis: no visible global function
  definition for ‘axis’
pipeline.2ndLvlCorrelationAnalysis : <anonymous>: no visible binding
  for global variable ‘group.labels’
pipeline.2ndLvlCorrelationAnalysis : <anonymous>: no visible global
  function definition for ‘hclust’
pipeline.2ndLvlCorrelationAnalysis : <anonymous>: no visible global
  function definition for ‘dist’
pipeline.2ndLvlCorrelationAnalysis: no visible global function
  definition for ‘dev.off’
pipeline.2ndLvlModuleCorrelation: no visible global function definition
  for ‘cor’
pipeline.2ndLvlModuleCorrelation: no visible global function definition
  for ‘quantile’
pipeline.2ndLvlModuleCorrelation: no visible binding for global
  variable ‘indata’
pipeline.2ndLvlModuleCorrelation: no visible global function definition
  for ‘layout’
pipeline.2ndLvlModuleCorrelation: no visible global function definition
  for ‘par’
pipeline.2ndLvlModuleCorrelation: no visible global function definition
  for ‘image’
pipeline.2ndLvlModuleCorrelation: no visible binding for global
  variable ‘group.colors’
pipeline.2ndLvlModuleCorrelation: no visible global function definition
  for ‘color.palette.heatmaps’
pipeline.2ndLvlModuleCorrelation: no visible global function definition
  for ‘box’
pipeline.2ndLvlModuleCorrelation : <anonymous>: no visible global
  function definition for ‘rect’
pipeline.2ndLvlModuleCorrelation: no visible binding for global
  variable ‘preferences’
pipeline.2ndLvlModuleCorrelation : <anonymous>: no visible global
  function definition for ‘sd’
pipeline.2ndLvlModuleCorrelation : <anonymous>: no visible global
  function definition for ‘text’
pipeline.2ndLvlModuleCorrelation: no visible global function definition
  for ‘as.dendrogram’
pipeline.2ndLvlModuleCorrelation: no visible global function definition
  for ‘title’
pipeline.2ndLvlSimilarityAnalysis: no visible binding for '<<-'
  assignment to ‘metagene.filter.list’
pipeline.2ndLvlSimilarityAnalysis: no visible binding for global
  variable ‘metagene.filter.list’
pipeline.2ndLvlSimilarityAnalysis: no visible binding for global
  variable ‘preferences’
pipeline.2ndLvlSimilarityAnalysis: no visible binding for global
  variable ‘metadata’
pipeline.2ndLvlSimilarityAnalysis: no visible binding for global
  variable ‘var’
pipeline.2ndLvlSimilarityAnalysis: no visible binding for global
  variable ‘files.name’
pipeline.2ndLvlSimilarityAnalysis: no visible global function
  definition for ‘pdf’
pipeline.2ndLvlSimilarityAnalysis: no visible global function
  definition for ‘par’
pipeline.2ndLvlSimilarityAnalysis: no visible global function
  definition for ‘dist’
pipeline.2ndLvlSimilarityAnalysis: no visible binding for global
  variable ‘indata’
pipeline.2ndLvlSimilarityAnalysis: no visible binding for global
  variable ‘group.colors’
pipeline.2ndLvlSimilarityAnalysis: no visible global function
  definition for ‘title’
pipeline.2ndLvlSimilarityAnalysis: no visible global function
  definition for ‘box’
pipeline.2ndLvlSimilarityAnalysis: no visible global function
  definition for ‘legend’
pipeline.2ndLvlSimilarityAnalysis: no visible binding for global
  variable ‘group.labels’
pipeline.2ndLvlSimilarityAnalysis: no visible binding for global
  variable ‘groupwise.group.colors’
pipeline.2ndLvlSimilarityAnalysis: no visible global function
  definition for ‘color.palette.heatmaps’
pipeline.2ndLvlSimilarityAnalysis: no visible global function
  definition for ‘image’
pipeline.2ndLvlSimilarityAnalysis: no visible global function
  definition for ‘axis’
pipeline.2ndLvlSimilarityAnalysis: no visible global function
  definition for ‘dev.off’
pipeline.2ndLvlSom: no visible binding for '<<-' assignment to
  ‘secLvlSom.custom’
pipeline.2ndLvlSom: no visible binding for global variable ‘metadata’
pipeline.2ndLvlSom: no visible binding for global variable
  ‘preferences’
pipeline.2ndLvlSom: no visible binding for '<<-' assignment to
  ‘secLvlSom.20.20’
pipeline.2ndLvlSom: no visible binding for global variable
  ‘secLvlSom.custom’
pipeline.2ndLvlSom: no visible binding for global variable ‘files.name’
pipeline.2ndLvlSom: no visible global function definition for ‘pdf’
pipeline.2ndLvlSom: no visible global function definition for ‘par’
pipeline.2ndLvlSom: no visible binding for global variable
  ‘group.labels’
pipeline.2ndLvlSom: no visible global function definition for ‘legend’
pipeline.2ndLvlSom: no visible binding for global variable
  ‘groupwise.group.colors’
pipeline.2ndLvlSom: no visible global function definition for ‘points’
pipeline.2ndLvlSom: no visible binding for global variable
  ‘group.colors’
pipeline.2ndLvlSom: no visible global function definition for ‘box’
pipeline.2ndLvlSom: no visible global function definition for ‘text’
pipeline.2ndLvlSom: no visible binding for global variable ‘indata’
pipeline.2ndLvlSom: no visible global function definition for ‘chull’
pipeline.2ndLvlSom: no visible global function definition for ‘polygon’
pipeline.2ndLvlSom: no visible binding for global variable
  ‘secLvlSom.20.20’
pipeline.2ndLvlSom: no visible global function definition for
  ‘color.palette.portraits’
pipeline.2ndLvlSom: no visible global function definition for ‘dev.off’
pipeline.3rdLvlChromosomalEnrichment: no visible binding for global
  variable ‘output.paths’
pipeline.3rdLvlChromosomalEnrichment: no visible binding for global
  variable ‘files.name’
pipeline.3rdLvlChromosomalEnrichment : plot.set.list.chromosomes: no
  visible binding for global variable ‘gene.positions’
pipeline.3rdLvlChromosomalEnrichment : plot.set.list.chromosomes: no
  visible binding for global variable ‘gene.positions.list’
pipeline.3rdLvlChromosomalEnrichment : plot.set.list.chromosomes: no
  visible global function definition for ‘write.csv2’
pipeline.3rdLvlChromosomalEnrichment : plot.set.list.chromosomes: no
  visible global function definition for ‘colorRampPalette’
pipeline.3rdLvlChromosomalEnrichment : plot.set.list.chromosomes: no
  visible binding for global variable ‘head’
pipeline.3rdLvlChromosomalEnrichment : plot.set.list.chromosomes: no
  visible global function definition for ‘par’
pipeline.3rdLvlChromosomalEnrichment : plot.set.list.chromosomes: no
  visible global function definition for ‘image’
pipeline.3rdLvlChromosomalEnrichment : plot.set.list.chromosomes: no
  visible global function definition for ‘title’
pipeline.3rdLvlChromosomalEnrichment : plot.set.list.chromosomes: no
  visible global function definition for ‘box’
pipeline.3rdLvlChromosomalEnrichment : plot.set.list.chromosomes: no
  visible global function definition for ‘abline’
pipeline.3rdLvlChromosomalEnrichment : plot.set.list.chromosomes: no
  visible global function definition for ‘axis’
pipeline.3rdLvlChromosomalEnrichment : plot.set.list.chromosomes: no
  visible global function definition for ‘layout’
pipeline.3rdLvlChromosomalEnrichment : plot.set.list.chromosomes: no
  visible global function definition for ‘text’
pipeline.3rdLvlChromosomalEnrichment: no visible global function
  definition for ‘pdf’
pipeline.3rdLvlChromosomalEnrichment: no visible binding for global
  variable ‘gene.positions.list’
pipeline.3rdLvlChromosomalEnrichment: no visible binding for global
  variable ‘spot.list.overexpression’
pipeline.3rdLvlChromosomalEnrichment: no visible global function
  definition for ‘dev.off’
pipeline.3rdLvlChromosomalEnrichment: no visible binding for global
  variable ‘spot.list.underexpression’
pipeline.3rdLvlChromosomalEnrichment: no visible binding for global
  variable ‘spot.list.kmeans’
pipeline.3rdLvlChromosomalEnrichment: no visible binding for global
  variable ‘group.labels’
pipeline.3rdLvlChromosomalEnrichment: no visible binding for global
  variable ‘spot.list.group.overexpression’
pipeline.3rdLvlChromosomalEnrichment: no visible binding for global
  variable ‘spot.list.dmap’
pipeline.3rdLvlNetworks : plot.set.list.networks: no visible global
  function definition for ‘sd’
pipeline.3rdLvlNetworks : plot.set.list.networks: no visible binding
  for global variable ‘metadata’
pipeline.3rdLvlNetworks : plot.set.list.networks: no visible global
  function definition for ‘cor’
pipeline.3rdLvlNetworks : plot.set.list.networks: no visible global
  function definition for ‘par’
pipeline.3rdLvlNetworks : plot.set.list.networks: no visible global
  function definition for ‘image’
pipeline.3rdLvlNetworks : plot.set.list.networks: no visible binding
  for global variable ‘preferences’
pipeline.3rdLvlNetworks : plot.set.list.networks: no visible global
  function definition for ‘rect’
pipeline.3rdLvlNetworks : plot.set.list.networks: no visible global
  function definition for ‘legend’
pipeline.3rdLvlNetworks: no visible binding for global variable
  ‘files.name’
pipeline.3rdLvlNetworks: no visible global function definition for
  ‘pdf’
pipeline.3rdLvlNetworks: no visible binding for global variable
  ‘spot.list.overexpression’
pipeline.3rdLvlNetworks: no visible global function definition for
  ‘dev.off’
pipeline.3rdLvlNetworks: no visible binding for global variable
  ‘spot.list.underexpression’
pipeline.3rdLvlNetworks: no visible binding for global variable
  ‘spot.list.kmeans’
pipeline.3rdLvlNetworks: no visible binding for global variable
  ‘group.labels’
pipeline.3rdLvlNetworks: no visible binding for global variable
  ‘spot.list.group.overexpression’
pipeline.3rdLvlNetworks: no visible binding for global variable
  ‘spot.list.dmap’
pipeline.3rdLvlSummarySheets : plot.set.list.reports: no visible global
  function definition for ‘sd’
pipeline.3rdLvlSummarySheets : plot.set.list.reports: no visible
  binding for global variable ‘group.labels’
pipeline.3rdLvlSummarySheets : plot.set.list.reports: no visible global
  function definition for ‘hist’
pipeline.3rdLvlSummarySheets : plot.set.list.reports: no visible
  binding for global variable ‘metadata’
pipeline.3rdLvlSummarySheets : plot.set.list.reports: no visible global
  function definition for ‘par’
pipeline.3rdLvlSummarySheets : plot.set.list.reports: no visible global
  function definition for ‘color.palette.portraits’
pipeline.3rdLvlSummarySheets : plot.set.list.reports: no visible global
  function definition for ‘colorRampPalette’
pipeline.3rdLvlSummarySheets : plot.set.list.reports: no visible global
  function definition for ‘image’
pipeline.3rdLvlSummarySheets : plot.set.list.reports: no visible
  binding for global variable ‘preferences’
pipeline.3rdLvlSummarySheets : plot.set.list.reports: no visible global
  function definition for ‘box’
pipeline.3rdLvlSummarySheets : plot.set.list.reports: no visible global
  function definition for ‘points’
pipeline.3rdLvlSummarySheets : plot.set.list.reports: no visible global
  function definition for ‘text’
pipeline.3rdLvlSummarySheets : plot.set.list.reports: no visible global
  function definition for ‘layout’
pipeline.3rdLvlSummarySheets : plot.set.list.reports: no visible global
  function definition for ‘axis’
pipeline.3rdLvlSummarySheets : plot.set.list.reports: no visible global
  function definition for ‘barplot’
pipeline.3rdLvlSummarySheets : plot.set.list.reports: no visible
  binding for global variable ‘group.colors’
pipeline.3rdLvlSummarySheets : plot.set.list.reports: no visible
  binding for global variable ‘indata’
pipeline.3rdLvlSummarySheets : plot.set.list.reports: no visible global
  function definition for ‘abline’
pipeline.3rdLvlSummarySheets : plot.set.list.reports: no visible
  binding for global variable ‘groupwise.group.colors’
pipeline.3rdLvlSummarySheets : plot.set.list.reports: no visible global
  function definition for ‘boxplot’
pipeline.3rdLvlSummarySheets : plot.set.list.reports: no visible global
  function definition for ‘legend’
pipeline.3rdLvlSummarySheets : plot.set.list.reports: no visible global
  function definition for ‘stars’
pipeline.3rdLvlSummarySheets : plot.set.list.reports : <anonymous>: no
  visible binding for global variable ‘group.labels’
pipeline.3rdLvlSummarySheets: no visible binding for global variable
  ‘files.name’
pipeline.3rdLvlSummarySheets: no visible global function definition for
  ‘pdf’
pipeline.3rdLvlSummarySheets: no visible binding for global variable
  ‘spot.list.overexpression’
pipeline.3rdLvlSummarySheets: no visible global function definition for
  ‘dev.off’
pipeline.3rdLvlSummarySheets: no visible binding for global variable
  ‘spot.list.underexpression’
pipeline.3rdLvlSummarySheets: no visible binding for global variable
  ‘spot.list.kmeans’
pipeline.3rdLvlSummarySheets: no visible binding for global variable
  ‘group.labels’
pipeline.3rdLvlSummarySheets: no visible binding for global variable
  ‘spot.list.group.overexpression’
pipeline.3rdLvlSummarySheets: no visible binding for global variable
  ‘spot.list.dmap’
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 ‘lines’
pipeline.calcStatistics: no visible binding for global variable
  ‘output.paths’
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 global function definition for
  ‘bmp’
pipeline.calcStatistics: no visible global function definition for
  ‘par’
pipeline.calcStatistics: no visible global function definition for
  ‘mtext’
pipeline.calcStatistics: no visible global function definition for
  ‘points’
pipeline.calcStatistics: no visible global function definition for
  ‘legend’
pipeline.calcStatistics: no visible global function definition for
  ‘dev.off’
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.nodes’
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.ids’
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.nodes’
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
  ‘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.chromosomeExpressionReports: no visible binding for global
  variable ‘metadata’
pipeline.chromosomeExpressionReports: no visible binding for global
  variable ‘gene.positions.list’
pipeline.chromosomeExpressionReports : <anonymous>: no visible binding
  for global variable ‘gene.ids’
pipeline.chromosomeExpressionReports: no visible binding for global
  variable ‘indata’
pipeline.chromosomeExpressionReports : <anonymous>: no visible binding
  for global variable ‘unique.protein.ids’
pipeline.chromosomeExpressionReports : <anonymous>: no visible binding
  for global variable ‘t.ensID.m’
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 ‘color.palette.heatmaps’
pipeline.chromosomeExpressionReports: no visible binding for global
  variable ‘group.colors’
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 ‘box’
pipeline.chromosomeExpressionReports: no visible global function
  definition for ‘axis’
pipeline.chromosomeExpressionReports: no visible global function
  definition for ‘title’
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.nodes’
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 binding for global variable
  ‘group.labels’
pipeline.differenceAnalyses: no visible global function definition for
  ‘combn’
pipeline.differenceAnalyses : <anonymous>: no visible binding for
  global variable ‘group.labels’
pipeline.differenceAnalyses: no visible binding for global variable
  ‘files.name’
pipeline.differenceAnalyses: no visible binding for '<<-' assignment to
  ‘WAD.g.m’
pipeline.differenceAnalyses: no visible binding for global variable
  ‘indata’
pipeline.differenceAnalyses: no visible binding for '<<-' assignment to
  ‘t.g.m’
pipeline.differenceAnalyses: no visible binding for '<<-' assignment to
  ‘p.g.m’
pipeline.differenceAnalyses: no visible binding for '<<-' assignment to
  ‘fdr.g.m’
pipeline.differenceAnalyses: no visible binding for '<<-' assignment to
  ‘Fdr.g.m’
pipeline.differenceAnalyses: no visible binding for '<<-' assignment to
  ‘n.0.m’
pipeline.differenceAnalyses: no visible binding for global variable
  ‘n.0.m’
pipeline.differenceAnalyses: no visible binding for '<<-' assignment to
  ‘perc.DE.m’
pipeline.differenceAnalyses: no visible binding for global variable
  ‘perc.DE.m’
pipeline.differenceAnalyses: no visible binding for global variable
  ‘metadata’
pipeline.differenceAnalyses: no visible binding for global variable
  ‘var’
pipeline.differenceAnalyses: no visible binding for global variable
  ‘t.g.m’
pipeline.differenceAnalyses: no visible binding for global variable
  ‘p.g.m’
pipeline.differenceAnalyses: no visible global function definition for
  ‘pt’
pipeline.differenceAnalyses: no visible binding for global variable
  ‘fdr.g.m’
pipeline.differenceAnalyses: no visible binding for global variable
  ‘Fdr.g.m’
pipeline.differenceAnalyses: no visible binding for global variable
  ‘WAD.g.m’
pipeline.differenceAnalyses: no visible binding for '<<-' assignment to
  ‘indata’
pipeline.differenceAnalyses: no visible binding for '<<-' assignment to
  ‘metadata’
pipeline.differenceAnalyses: no visible binding for '<<-' assignment to
  ‘group.labels’
pipeline.differenceAnalyses: no visible binding for '<<-' assignment to
  ‘group.colors’
pipeline.differenceAnalyses: no visible binding for global variable
  ‘group.colors’
pipeline.differenceAnalyses: no visible binding for '<<-' assignment to
  ‘output.paths’
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
  ‘output.paths’
pipeline.geneLists: no visible binding for global variable ‘indata’
pipeline.geneLists: no visible binding for global variable ‘p.g.m’
pipeline.geneLists: no visible binding for global variable ‘gene.names’
pipeline.geneLists: no visible binding for global variable ‘files.name’
pipeline.geneLists: no visible binding for global variable
  ‘gs.def.list’
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
  ‘gene.coordinates’
pipeline.geneLists: no visible binding for global variable
  ‘gene.positions’
pipeline.geneLists: no visible binding for global variable
  ‘gene.descriptions’
pipeline.geneLists: no visible binding for global variable ‘perc.DE.m’
pipeline.geneLists: no visible global function definition for
  ‘write.csv2’
pipeline.geneLists: no visible binding for global variable
  ‘preferences’
pipeline.geneLists: no visible binding for global variable
  ‘spot.list.samples’
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
  ‘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.ids’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
  ‘sd’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
  ‘gene.names’
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.nodes’
pipeline.genesetProfilesAndMaps: no visible global function definition
  for ‘na.omit’
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 binding for global variable
  ‘gene.coordinates’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
  ‘gene.descriptions’
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.ids’
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 global
  variable ‘indata’
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 ‘gene.ids’
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.genesetStatisticSamples: no visible binding for global
  variable ‘output.paths’
pipeline.genesetStatisticSamples: no visible global function definition
  for ‘write.csv2’
pipeline.genesetStatisticSamples: no visible binding for global
  variable ‘samples.GSZ.scores’
pipeline.groupAnalysis: no visible binding for global variable
  ‘group.labels’
pipeline.groupAnalysis: no visible binding for global variable
  ‘files.name’
pipeline.groupAnalysis: no visible binding for '<<-' assignment to
  ‘WAD.g.m’
pipeline.groupAnalysis: no visible binding for global variable ‘indata’
pipeline.groupAnalysis: no visible binding for '<<-' assignment to
  ‘t.g.m’
pipeline.groupAnalysis: no visible binding for '<<-' assignment to
  ‘p.g.m’
pipeline.groupAnalysis: no visible binding for '<<-' assignment to
  ‘fdr.g.m’
pipeline.groupAnalysis: no visible binding for '<<-' assignment to
  ‘Fdr.g.m’
pipeline.groupAnalysis: no visible binding for '<<-' assignment to
  ‘n.0.m’
pipeline.groupAnalysis: no visible binding for global variable ‘n.0.m’
pipeline.groupAnalysis: no visible binding for '<<-' assignment to
  ‘perc.DE.m’
pipeline.groupAnalysis: no visible binding for global variable
  ‘perc.DE.m’
pipeline.groupAnalysis: no visible binding for global variable ‘t.g.m’
pipeline.groupAnalysis : <anonymous>: no visible global function
  definition for ‘sd’
pipeline.groupAnalysis: no visible binding for global variable ‘p.g.m’
pipeline.groupAnalysis: no visible global function definition for ‘pt’
pipeline.groupAnalysis: no visible binding for global variable
  ‘fdr.g.m’
pipeline.groupAnalysis: no visible binding for global variable
  ‘Fdr.g.m’
pipeline.groupAnalysis: no visible binding for global variable
  ‘WAD.g.m’
pipeline.groupAnalysis: no visible binding for '<<-' assignment to
  ‘metadata’
pipeline.groupAnalysis: no visible binding for global variable
  ‘metadata’
pipeline.groupAnalysis: no visible binding for '<<-' assignment to
  ‘indata’
pipeline.groupAnalysis: no visible binding for global variable
  ‘indata.gene.mean’
pipeline.groupAnalysis: no visible binding for '<<-' assignment to
  ‘indata.gene.mean’
pipeline.groupAnalysis: no visible binding for '<<-' assignment to
  ‘group.colors’
pipeline.groupAnalysis: no visible binding for global variable
  ‘group.colors’
pipeline.groupAnalysis: no visible binding for '<<-' assignment to
  ‘group.labels’
pipeline.groupAnalysis: no visible binding for '<<-' assignment to
  ‘output.paths’
pipeline.groupAssignment: no visible binding for global variable
  ‘group.labels’
pipeline.groupAssignment: no visible binding for global variable
  ‘files.name’
pipeline.groupAssignment: no visible binding for global variable
  ‘preferences’
pipeline.groupAssignment: no visible binding for global variable
  ‘pat.labels’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
  ‘opt.cluster.number’
pipeline.groupAssignment: no visible binding for global variable
  ‘opt.cluster.number’
pipeline.groupAssignment: no visible binding for global variable
  ‘indata’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
  ‘group.labels’
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.nodes’
pipeline.groupSpecificGenesets: no visible binding for global variable
  ‘gene.ids’
pipeline.groupSpecificGenesets: no visible binding for global variable
  ‘gs.def.list’
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.htmlIntegralSummary: no visible binding for global variable
  ‘files.name’
pipeline.htmlIntegralSummary: no visible binding for global variable
  ‘spot.list.overexpression’
pipeline.htmlIntegralSummary: no visible binding for global variable
  ‘group.labels’
pipeline.htmlIntegralSummary: no visible binding for global variable
  ‘spot.list.group.overexpression’
pipeline.htmlIntegralSummary: no visible binding for global variable
  ‘spot.list.underexpression’
pipeline.htmlIntegralSummary: no visible binding for global variable
  ‘spot.list.correlation’
pipeline.htmlIntegralSummary: no visible binding for global variable
  ‘spot.list.kmeans’
pipeline.htmlIntegralSummary: no visible binding for global variable
  ‘spot.list.dmap’
pipeline.htmlSampleSummary: no visible binding for global variable
  ‘files.name’
pipeline.htmlSampleSummary: no visible binding for global variable
  ‘group.labels’
pipeline.htmlSampleSummary: no visible binding for global variable
  ‘indata’
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.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.prepare: no visible binding for global variable ‘preferences’
pipeline.prepare: no visible binding for '<<-' assignment to
  ‘preferences’
pipeline.prepare : <anonymous>: no visible binding for global variable
  ‘indata’
pipeline.prepare : <anonymous> : <anonymous>: no visible global
  function definition for ‘na.omit’
pipeline.prepare: no visible binding for global variable ‘indata’
pipeline.prepare: no visible binding for '<<-' assignment to
  ‘group.labels’
pipeline.prepare: no visible binding for '<<-' assignment to
  ‘group.colors’
pipeline.prepare: no visible binding for '<<-' assignment to ‘indata’
pipeline.prepare: no visible binding for global variable ‘group.labels’
pipeline.prepare: no visible binding for global variable ‘group.colors’
pipeline.prepare: no visible binding for '<<-' assignment to
  ‘files.name’
pipeline.prepare: no visible binding for global variable ‘files.name’
pipeline.prepare: no visible binding for '<<-' assignment to
  ‘output.paths’
pipeline.prepare: no visible binding for global variable
  ‘color.palette.portraits’
pipeline.prepare: no visible binding for '<<-' assignment to
  ‘color.palette.portraits’
pipeline.prepare: no visible global function definition for
  ‘colorRampPalette’
pipeline.prepare: no visible binding for global variable
  ‘color.palette.heatmaps’
pipeline.prepare: no visible binding for '<<-' assignment to
  ‘color.palette.heatmaps’
pipeline.prepare: no visible global function definition for ‘col2rgb’
pipeline.prepare : <anonymous>: no visible global function definition
  for ‘rgb’
pipeline.prepare: no visible binding for '<<-' assignment to
  ‘groupwise.group.colors’
pipeline.prepare: no visible binding for global variable
  ‘groupwise.group.colors’
pipeline.prepare: no visible binding for '<<-' assignment to
  ‘indata.sample.mean’
pipeline.prepare: no visible binding for '<<-' assignment to
  ‘indata.gene.mean’
pipeline.prepare: no visible binding for global variable
  ‘indata.gene.mean’
pipeline.prepare: no visible binding for '<<-' assignment to
  ‘som.result’
pipeline.prepare: no visible binding for global variable ‘som.result’
pipeline.prepare: no visible binding for '<<-' assignment to ‘metadata’
pipeline.prepare: no visible binding for global variable ‘metadata’
pipeline.prepare: no visible binding for '<<-' assignment to
  ‘gene.coordinates’
pipeline.prepare: no visible binding for global variable
  ‘gene.coordinates’
pipeline.prepare: no visible binding for '<<-' assignment to
  ‘som.nodes’
pipeline.prepare: no visible binding for global variable ‘som.nodes’
pipeline.prepare: no visible binding for global variable ‘gene.names’
pipeline.prepare: no visible binding for global variable
  ‘gene.positions’
pipeline.prepare: no visible binding for global variable
  ‘gene.descriptions’
pipeline.prepare: no visible global function definition for
  ‘write.csv2’
pipeline.prepareAnnotation: no visible binding for '<<-' assignment to
  ‘gene.ids’
pipeline.prepareAnnotation: no visible binding for global variable
  ‘indata’
pipeline.prepareAnnotation: no visible binding for global variable
  ‘gene.ids’
pipeline.prepareAnnotation: no visible binding for '<<-' assignment to
  ‘gene.names’
pipeline.prepareAnnotation: no visible binding for global variable
  ‘gene.names’
pipeline.prepareAnnotation: no visible binding for '<<-' assignment to
  ‘gene.descriptions’
pipeline.prepareAnnotation: no visible binding for global variable
  ‘gene.descriptions’
pipeline.prepareAnnotation: no visible binding for '<<-' assignment to
  ‘gene.positions’
pipeline.prepareAnnotation: no visible binding for global variable
  ‘gene.positions’
pipeline.prepareAnnotation: no visible binding for '<<-' assignment to
  ‘gene.positions.table’
pipeline.prepareAnnotation: no visible binding for '<<-' assignment to
  ‘gene.positions.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.positions.table’
pipeline.prepareAnnotation: no visible binding for global variable
  ‘gene.positions.list’
pipeline.prepareAnnotation : <anonymous>: no visible binding for global
  variable ‘gene.positions.table’
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.ids’
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.qualityCheck: no visible binding for global variable
  ‘output.paths’
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 ‘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 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
  ‘indata.sample.mean’
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 ‘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.sampleRankMaps: no visible binding for global variable
  ‘files.name’
pipeline.sampleRankMaps: no visible global function definition for
  ‘pdf’
pipeline.sampleRankMaps: no visible global function definition for
  ‘par’
pipeline.sampleRankMaps: no visible global function definition for
  ‘text’
pipeline.sampleRankMaps: no visible binding for global variable
  ‘group.labels’
pipeline.sampleRankMaps: no visible global function definition for
  ‘mtext’
pipeline.sampleRankMaps: no visible binding for global variable
  ‘groupwise.group.colors’
pipeline.sampleRankMaps: no visible binding for global variable
  ‘indata’
pipeline.sampleRankMaps: no visible binding for global variable
  ‘som.nodes’
pipeline.sampleRankMaps: no visible binding for global variable
  ‘preferences’
pipeline.sampleRankMaps: no visible global function definition for
  ‘image’
pipeline.sampleRankMaps: no visible global function definition for
  ‘color.palette.portraits’
pipeline.sampleRankMaps: no visible global function definition for
  ‘title’
pipeline.sampleRankMaps: no visible global function definition for
  ‘box’
pipeline.sampleRankMaps: no visible binding for global variable
  ‘WAD.g.m’
pipeline.sampleRankMaps: no visible binding for global variable ‘t.g.m’
pipeline.sampleRankMaps: 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
  ‘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.summarySheetsIntegral : plot.set.list: no visible global
  function definition for ‘pdf’
pipeline.summarySheetsIntegral : plot.set.list: no visible global
  function definition for ‘layout’
pipeline.summarySheetsIntegral : plot.set.list: no visible global
  function definition for ‘par’
pipeline.summarySheetsIntegral : plot.set.list: no visible global
  function definition for ‘color.palette.portraits’
pipeline.summarySheetsIntegral : plot.set.list: no visible global
  function definition for ‘colorRampPalette’
pipeline.summarySheetsIntegral : plot.set.list: no visible global
  function definition for ‘image’
pipeline.summarySheetsIntegral : plot.set.list: no visible binding for
  global variable ‘preferences’
pipeline.summarySheetsIntegral : plot.set.list: no visible global
  function definition for ‘mtext’
pipeline.summarySheetsIntegral : plot.set.list: no visible global
  function definition for ‘box’
pipeline.summarySheetsIntegral : plot.set.list: no visible global
  function definition for ‘color.palette.heatmaps’
pipeline.summarySheetsIntegral : plot.set.list: no visible global
  function definition for ‘axis’
pipeline.summarySheetsIntegral : plot.set.list: no visible global
  function definition for ‘points’
pipeline.summarySheetsIntegral : plot.set.list: no visible global
  function definition for ‘text’
pipeline.summarySheetsIntegral : plot.set.list : <anonymous>: no
  visible global function definition for ‘head’
pipeline.summarySheetsIntegral : plot.set.list: no visible global
  function definition for ‘legend’
pipeline.summarySheetsIntegral : plot.set.list: no visible binding for
  global variable ‘indata’
pipeline.summarySheetsIntegral : plot.set.list: no visible binding for
  global variable ‘group.labels’
pipeline.summarySheetsIntegral : plot.set.list: no visible binding for
  global variable ‘group.colors’
pipeline.summarySheetsIntegral : plot.set.list: no visible global
  function definition for ‘frame’
pipeline.summarySheetsIntegral : plot.set.list: no visible binding for
  global variable ‘samples.GSZ.scores’
pipeline.summarySheetsIntegral : plot.set.list: no visible global
  function definition for ‘sd’
pipeline.summarySheetsIntegral : plot.set.list: no visible global
  function definition for ‘cor’
pipeline.summarySheetsIntegral : plot.set.list: no visible binding for
  global variable ‘metadata’
pipeline.summarySheetsIntegral : plot.set.list: no visible global
  function definition for ‘barplot’
pipeline.summarySheetsIntegral : plot.set.list : <anonymous>: no
  visible binding for global variable ‘indata’
pipeline.summarySheetsIntegral : plot.set.list : <anonymous>: no
  visible global function definition for ‘cor’
pipeline.summarySheetsIntegral : plot.set.list: no visible global
  function definition for ‘rect’
pipeline.summarySheetsIntegral : plot.set.list: no visible binding for
  global variable ‘gene.names’
pipeline.summarySheetsIntegral : plot.set.list: no visible binding for
  global variable ‘gene.descriptions’
pipeline.summarySheetsIntegral : plot.set.list: no visible binding for
  global variable ‘gs.def.list’
pipeline.summarySheetsIntegral : plot.set.list : <anonymous>: no
  visible binding for global variable ‘gene.ids’
pipeline.summarySheetsIntegral : plot.set.list: no visible global
  function definition for ‘hist’
pipeline.summarySheetsIntegral : plot.set.list: no visible global
  function definition for ‘abline’
pipeline.summarySheetsIntegral : plot.set.list: no visible global
  function definition for ‘lines’
pipeline.summarySheetsIntegral : plot.set.list: no visible global
  function definition for ‘dev.off’
pipeline.summarySheetsIntegral : csv.set.list : <anonymous>: no visible
  binding for global variable ‘indata’
pipeline.summarySheetsIntegral : csv.set.list : <anonymous>: no visible
  global function definition for ‘cor’
pipeline.summarySheetsIntegral : csv.set.list: no visible binding for
  global variable ‘indata’
pipeline.summarySheetsIntegral : csv.set.list: no visible global
  function definition for ‘pt’
pipeline.summarySheetsIntegral : csv.set.list: no visible binding for
  global variable ‘gene.names’
pipeline.summarySheetsIntegral : csv.set.list: no visible binding for
  global variable ‘files.name’
pipeline.summarySheetsIntegral : csv.set.list: no visible binding for
  global variable ‘gs.def.list’
pipeline.summarySheetsIntegral : csv.set.list: no visible binding for
  global variable ‘indata.gene.mean’
pipeline.summarySheetsIntegral : csv.set.list: no visible binding for
  global variable ‘sd’
pipeline.summarySheetsIntegral : csv.set.list: no visible binding for
  global variable ‘gene.coordinates’
pipeline.summarySheetsIntegral : csv.set.list: no visible binding for
  global variable ‘gene.positions’
pipeline.summarySheetsIntegral : csv.set.list: no visible binding for
  global variable ‘gene.descriptions’
pipeline.summarySheetsIntegral : csv.set.list: no visible global
  function definition for ‘write.csv2’
pipeline.summarySheetsIntegral: no visible binding for global variable
  ‘spot.list.overexpression’
pipeline.summarySheetsIntegral: no visible binding for global variable
  ‘spot.list.underexpression’
pipeline.summarySheetsIntegral: no visible binding for global variable
  ‘spot.list.correlation’
pipeline.summarySheetsIntegral: no visible binding for global variable
  ‘spot.list.kmeans’
pipeline.summarySheetsIntegral: no visible binding for global variable
  ‘spot.list.dmap’
pipeline.summarySheetsIntegral: no visible binding for global variable
  ‘group.labels’
pipeline.summarySheetsIntegral: no visible binding for global variable
  ‘spot.list.group.overexpression’
pipeline.summarySheetsIntegral: 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
  ‘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
  ‘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.ids’
pipeline.summarySheetsSamples: no visible binding for global variable
  ‘indata’
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 ‘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 binding for global variable
  ‘gene.coordinates’
pipeline.summarySheetsSamples: no visible binding for global variable
  ‘gene.descriptions’
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 binding for global variable
  ‘som.nodes’
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 global function
  definition for ‘hist’
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 ‘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’
smoothScatter: no visible global function definition for
  ‘colorRampPalette’
smoothScatter: no visible binding for global variable ‘blues9’
smoothScatter: no visible binding for global variable ‘box’
smoothScatter: no visible global function definition for ‘par’
smoothScatter: no visible global function definition for ‘xy.coords’
smoothScatter: no visible global function definition for ‘image’
smoothScatter: 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 aov arrows as.dendrogram axis barplot blues9
  bmp box boxplot chull col2rgb color.palette.heatmaps
  color.palette.portraits colorRampPalette combn cor cutree data
  density dev.off dist ecdf fdr.g.m files.name fisher.test
  flush.console frame gene.coordinates gene.descriptions gene.ids
  gene.names gene.positions gene.positions.list gene.positions.table
  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 metagene.filter.list modifyList mtext n.0.m na.omit
  opossom.genesets opt.cluster.number order.dendrogram output.paths
  p.g.m p.m par parSapply pat.labels pbeta pdf perc.DE.m persp pie
  points polygon preferences pt quantile rect reorder rgb
  samples.GSZ.scores sd secLvlSom.20.20 secLvlSom.custom sessionInfo
  som.nodes som.result spot.list.correlation spot.list.dmap
  spot.list.group.overexpression spot.list.kmeans
  spot.list.overexpression spot.list.samples spot.list.underexpression
  stars t.ensID.m t.g.m t.m text title unique.protein.ids var
  wilcox.test write.csv2 xy.coords
Consider adding
  importFrom("grDevices", "blues9", "bmp", "chull", "col2rgb",
             "colorRampPalette", "dev.off", "pdf", "rgb", "xy.coords")
  importFrom("graphics", "abline", "arrows", "axis", "barplot", "box",
             "boxplot", "frame", "hist", "image", "layout", "legend",
             "lines", "mtext", "par", "persp", "pie", "points",
             "polygon", "rect", "stars", "text", "title")
  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.
* 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 sizes of PDF files under ‘inst/doc’ ... 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 21.56  0.196  45.150
opossom.run      6.30  0.056  27.445
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/oposSOM.Rcheck/00check.log’
for details.


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)

oposSOM.Rcheck/oposSOM-Ex.timings:

nameusersystemelapsed
oposSOM-package21.560 0.19645.150
opossom.new0.0760.0000.077
opossom.run 6.300 0.05627.445