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BioC 3.0: CHECK report for oposSOM on perceval

This page was generated on 2015-04-10 09:59:59 -0700 (Fri, 10 Apr 2015).

Package 627/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
oposSOM 1.1.1
Henry Wirth
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/oposSOM
Last Changed Rev: 98264 / Revision: 102249
Last Changed Date: 2015-01-12 03:51:41 -0800 (Mon, 12 Jan 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: oposSOM
Version: 1.1.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch oposSOM_1.1.1.tar.gz
StartedAt: 2015-04-10 04:30:00 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 04:35:38 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 337.6 seconds
RetCode: 0
Status:  OK 
CheckDir: oposSOM.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch oposSOM_1.1.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/oposSOM.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘oposSOM/DESCRIPTION’ ... OK
* this is package ‘oposSOM’ version ‘1.1.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘oposSOM’ can be installed ... [17s/18s] 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
pipeline.2ndLvlComponentAnalysis: no visible binding for global
  variable ‘files.name’
pipeline.2ndLvlComponentAnalysis: no visible binding for global
  variable ‘metagene.filter.list’
pipeline.2ndLvlComponentAnalysis: no visible binding for global
  variable ‘metadata’
pipeline.2ndLvlComponentAnalysis: no visible binding for global
  variable ‘group.colors’
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 binding for global
  variable ‘indata’
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 ‘files.name’
pipeline.2ndLvlCorrelationAnalysis: no visible binding for global
  variable ‘metagene.filter.list’
pipeline.2ndLvlCorrelationAnalysis: no visible binding for global
  variable ‘metadata’
pipeline.2ndLvlCorrelationAnalysis: no visible binding for global
  variable ‘indata’
pipeline.2ndLvlCorrelationAnalysis: no visible binding for global
  variable ‘group.labels’
pipeline.2ndLvlCorrelationAnalysis: no visible binding for global
  variable ‘groupwise.group.colors’
pipeline.2ndLvlCorrelationAnalysis: no visible global function
  definition for ‘colramp’
pipeline.2ndLvlCorrelationAnalysis : <anonymous>: no visible binding
  for global variable ‘group.labels’
pipeline.2ndLvlModuleCorrelation: no visible binding for global
  variable ‘indata’
pipeline.2ndLvlModuleCorrelation: no visible binding for global
  variable ‘group.colors’
pipeline.2ndLvlModuleCorrelation: no visible global function definition
  for ‘colramp’
pipeline.2ndLvlModuleCorrelation : <anonymous>: no visible binding for
  global variable ‘spot.list.overexpression’
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 ‘spot.list.overexpression’
pipeline.2ndLvlSimilarityAnalysis: no visible binding for global
  variable ‘metadata’
pipeline.2ndLvlSimilarityAnalysis: no visible binding for global
  variable ‘files.name’
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 ‘colramp’
pipeline.2ndLvlSimilarityAnalysis: no visible binding for global
  variable ‘group.labels’
pipeline.2ndLvlSimilarityAnalysis: no visible binding for global
  variable ‘groupwise.group.colors’
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 binding for global variable ‘indata’
pipeline.2ndLvlSom: no visible binding for global variable
  ‘group.colors’
pipeline.2ndLvlSom: no visible binding for global variable
  ‘group.labels’
pipeline.2ndLvlSom: no visible binding for global variable
  ‘groupwise.group.colors’
pipeline.2ndLvlSom: no visible binding for global variable
  ‘secLvlSom.20.20’
pipeline.2ndLvlSom: no visible global function definition for ‘colramp’
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: no visible binding for global
  variable ‘gene.positions.list’
pipeline.3rdLvlChromosomalEnrichment: no visible binding for global
  variable ‘spot.list.overexpression’
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.3rdLvlChromosomeAssociationMaps: no visible binding for global
  variable ‘gene.positions’
pipeline.3rdLvlChromosomeAssociationMaps: no visible binding for global
  variable ‘set.list’
pipeline.3rdLvlChromosomeAssociationMaps : <anonymous>: no visible
  binding for global variable ‘gene.positions’
pipeline.3rdLvlChromosomeAssociationMaps: no visible binding for global
  variable ‘group.labels’
pipeline.3rdLvlChromosomeAssociationMaps: no visible binding for global
  variable ‘indata’
pipeline.3rdLvlChromosomeAssociationMaps: no visible binding for global
  variable ‘group.colors’
pipeline.3rdLvlChromosomeAssociationMaps: no visible binding for global
  variable ‘preferences’
pipeline.3rdLvlChromosomeAssociationMaps: no visible binding for global
  variable ‘intersect.counts’
pipeline.3rdLvlChromosomeAssociationMaps: no visible binding for global
  variable ‘colkey’
pipeline.3rdLvlChromosomeAssociationMaps: no visible binding for global
  variable ‘chr.sep.level’
pipeline.3rdLvlChromosomeAssociationMaps: no visible binding for global
  variable ‘chr.lab.level’
pipeline.3rdLvlChromosomeAssociationMaps: no visible binding for global
  variable ‘chr’
pipeline.3rdLvlChromosomeAssociationMaps : <anonymous>: no visible
  binding for global variable ‘set.list’
pipeline.3rdLvlNetworks : plot.set.list.networks: no visible binding
  for global variable ‘metadata’
pipeline.3rdLvlNetworks : plot.set.list.networks: no visible binding
  for global variable ‘indata’
pipeline.3rdLvlNetworks : plot.set.list.networks: no visible binding
  for global variable ‘group.labels’
pipeline.3rdLvlNetworks : plot.set.list.networks: no visible binding
  for global variable ‘preferences’
pipeline.3rdLvlNetworks : plot.set.list.networks: no visible binding
  for global variable ‘group.colors’
pipeline.3rdLvlNetworks : plot.set.list.networks: no visible binding
  for global variable ‘groupwise.group.colors’
pipeline.3rdLvlNetworks: no visible binding for global variable
  ‘files.name’
pipeline.3rdLvlNetworks: no visible binding for global variable
  ‘spot.list.overexpression’
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.3rdLvlNetworksWto: no visible binding for global variable
  ‘preferences’
pipeline.3rdLvlNetworksWto: no visible binding for global variable
  ‘weight’
pipeline.3rdLvlSummarySheets : plot.set.list.reports: no visible
  binding for global variable ‘group.labels’
pipeline.3rdLvlSummarySheets : plot.set.list.reports: no visible
  binding for global variable ‘metadata’
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 ‘colramp’
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
  binding for global variable ‘groupwise.group.colors’
pipeline.3rdLvlSummarySheets : plot.set.list.reports : <anonymous>: no
  visible binding for global variable ‘group.labels’
pipeline.3rdLvlSummarySheets : plot.set.list.reports: no visible
  binding for global variable ‘spot.list.samples’
pipeline.3rdLvlSummarySheets : plot.set.list.reports: no visible
  binding for global variable ‘gs.def.list.categories’
pipeline.3rdLvlSummarySheets: no visible binding for global variable
  ‘files.name’
pipeline.3rdLvlSummarySheets: no visible binding for global variable
  ‘spot.list.overexpression’
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.affymetrixQualityCheck: no visible binding for global variable
  ‘indata’
pipeline.affymetrixQualityCheck: no visible binding for global variable
  ‘group.colors’
pipeline.affymetrixQualityCheck: no visible binding for global variable
  ‘group.labels’
pipeline.affymetrixQualityCheck: no visible binding for global variable
  ‘groupwise.group.colors’
pipeline.calcStatistics: no visible binding for global variable
  ‘output.paths’
pipeline.calcStatistics: no visible binding for global variable
  ‘preferences’
pipeline.calcStatistics: no visible binding for global variable
  ‘indata.original’
pipeline.calcStatistics: no visible binding for global variable
  ‘indata’
pipeline.calcStatistics: no visible binding for '<<-' assignment to
  ‘sd.g.m’
pipeline.calcStatistics: no visible binding for '<<-' assignment to
  ‘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
  ‘WAD.g.m’
pipeline.calcStatistics : <anonymous>: no visible binding for global
  variable ‘indata.original’
pipeline.calcStatistics: no visible binding for global variable
  ‘sd.g.m’
pipeline.calcStatistics: no visible binding for global variable ‘t.g.m’
pipeline.calcStatistics : <anonymous>: no visible binding for global
  variable ‘sd.g.m’
pipeline.calcStatistics: no visible binding for global variable
  ‘group.labels’
pipeline.calcStatistics : <anonymous>: no visible binding for global
  variable ‘group.labels’
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 '<<-' assignment to
  ‘fdr.m’
pipeline.calcStatistics: no visible binding for global variable
  ‘som.nodes’
pipeline.calcStatistics: no visible binding for global variable ‘t.m’
pipeline.calcStatistics: no visible binding for global variable ‘p.m’
pipeline.calcStatistics: no visible binding for global variable ‘fdr.m’
pipeline.calcStatistics: no visible binding for global variable
  ‘group.colors’
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
  ‘preferences’
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
  ‘spot.list.overexpression’
pipeline.cancerHallmarks: no visible binding for global variable
  ‘files.name’
pipeline.cancerHallmarks: no visible binding for global variable
  ‘group.labels’
pipeline.cancerHallmarks: no visible binding for global variable
  ‘groupwise.group.colors’
pipeline.cancerHallmarks: no visible binding for global variable
  ‘som.nodes’
pipeline.cancerHallmarks: no visible global function definition for
  ‘colramp’
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 ‘preferences’
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 binding for global
  variable ‘group.colors’
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 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 global variable
  ‘group.metadata’
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 ‘group.metadata’
pipeline.detectSpotsIntegral : <anonymous>: no visible binding for
  global variable ‘preferences’
pipeline.detectSpotsSamples: no visible binding for '<<-' assignment to
  ‘spot.list.samples’
pipeline.detectSpotsSamples: no visible binding for global variable
  ‘indata’
pipeline.detectSpotsSamples: no visible binding for global variable
  ‘spot.list.samples’
pipeline.detectSpotsSamples: no visible binding for global variable
  ‘preferences’
pipeline.detectSpotsSamples: no visible binding for global variable
  ‘metadata’
pipeline.detectSpotsSamples: no visible binding for global variable
  ‘som.nodes’
pipeline.differenceAnalyses: no visible binding for global variable
  ‘group.labels’
pipeline.differenceAnalyses : <anonymous>: no visible binding for
  global variable ‘group.labels’
pipeline.differenceAnalyses: no visible binding for global variable
  ‘preferences’
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 '<<-' assignment to
  ‘indata’
pipeline.differenceAnalyses: no visible binding for '<<-' assignment to
  ‘metadata’
pipeline.differenceAnalyses: no visible binding for global variable
  ‘metadata’
pipeline.differenceAnalyses: no visible binding for global variable
  ‘indata.original’
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 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
  ‘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 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 binding for global variable
  ‘group.labels’
pipeline.entropyProfiles: no visible binding for global variable
  ‘groupwise.group.colors’
pipeline.entropyProfiles : <anonymous>: no visible binding for global
  variable ‘preferences’
pipeline.entropyProfiles: no visible binding for global variable
  ‘som.result’
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 binding for global variable
  ‘spot.list.samples’
pipeline.geneLists: no visible binding for global variable ‘metadata’
pipeline.geneLists: no visible binding for global variable
  ‘preferences’
pipeline.genesetOverviews: no visible binding for global variable
  ‘files.name’
pipeline.genesetOverviews: no visible binding for global variable
  ‘spot.list.samples’
pipeline.genesetOverviews : <anonymous> : <anonymous>: no visible
  binding for global variable ‘gs.def.list’
pipeline.genesetOverviews: no visible binding for global variable
  ‘spot.list.overexpression’
pipeline.genesetOverviews : <anonymous>: no visible binding for global
  variable ‘gs.def.list’
pipeline.genesetOverviews: no visible binding for global variable
  ‘gs.def.list.categories’
pipeline.genesetOverviews: no visible binding for global variable
  ‘indata’
pipeline.genesetOverviews: no visible binding for global variable
  ‘group.colors’
pipeline.genesetOverviews: no visible binding for global variable
  ‘group.labels’
pipeline.genesetOverviews : <anonymous>: no visible binding for global
  variable ‘group.labels’
pipeline.genesetOverviews: no visible binding for global variable
  ‘preferences’
pipeline.genesetProfilesAndMaps: no visible binding for '<<-'
  assignment to ‘samples.GSZ.scores’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
  ‘spot.list.samples’
pipeline.genesetProfilesAndMaps : <anonymous>: no visible binding for
  global variable ‘gs.def.list’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
  ‘files.name’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
  ‘samples.GSZ.scores’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
  ‘gs.def.list’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
  ‘preferences’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
  ‘som.nodes’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
  ‘gene.ids’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
  ‘group.colors’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
  ‘indata’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
  ‘group.labels’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
  ‘groupwise.group.colors’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
  ‘spot.list.overexpression’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
  ‘spot.list.kmeans’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
  ‘gene.coordinates’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
  ‘gene.names’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
  ‘gene.descriptions’
pipeline.genesetProfilesAndMaps: no visible global function definition
  for ‘colramp’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
  ‘som.result’
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 global
  variable ‘preferences’
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.genesetStatisticSamples: no visible binding for global
  variable ‘indata’
pipeline.genesetStatisticSamples: no visible binding for global
  variable ‘preferences’
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 ‘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 : <anonymous>: no visible binding for
  global variable ‘spot.list.samples’
pipeline.genesetStatisticSamples : <anonymous>: no visible binding for
  global variable ‘gene.ids’
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 ‘gs.def.list’
pipeline.genesetStatisticSamples : <anonymous>: no visible binding for
  global variable ‘preferences’
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 global variable
  ‘preferences’
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.original’
pipeline.groupAnalysis: no visible binding for global variable
  ‘indata.original’
pipeline.groupAnalysis: no visible binding for '<<-' assignment to
  ‘indata’
pipeline.groupAnalysis: no visible binding for '<<-' assignment to
  ‘indata.gene.mean’
pipeline.groupAnalysis: no visible binding for global variable ‘indata’
pipeline.groupAnalysis: no visible binding for global variable
  ‘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.groupAnalysis: no visible binding for '<<-' assignment to
  ‘preferences’
pipeline.groupAssignment: no visible binding for global variable
  ‘group.labels’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
  ‘group.bootstrap.score’
pipeline.groupAssignment: no visible binding for global variable
  ‘indata’
pipeline.groupAssignment: no visible binding for global variable
  ‘metadata’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
  ‘group.silhouette.coef’
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 binding for global variable
  ‘group.labels’
pipeline.groupSpecificGenesets: no visible binding for global variable
  ‘spot.list.samples’
pipeline.groupSpecificGenesets : <anonymous>: no visible binding for
  global variable ‘gs.def.list’
pipeline.groupSpecificGenesets : <anonymous>: no visible binding for
  global variable ‘group.labels’
pipeline.groupSpecificGenesets: no visible binding for global variable
  ‘files.name’
pipeline.groupSpecificGenesets: no visible binding for global variable
  ‘group.colors’
pipeline.groupSpecificGenesets: no visible binding for global variable
  ‘indata’
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 ‘colramp’
pipeline.htmlDifferencesSummary: no visible binding for global variable
  ‘files.name’
pipeline.htmlDifferencesSummary: no visible binding for global variable
  ‘indata’
pipeline.htmlDifferencesSummary: no visible binding for global variable
  ‘spot.list.samples’
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.htmlGenesetAnalysis: no visible binding for global variable
  ‘gs.def.list.categories’
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.htmlGroupSummary: no visible binding for global variable
  ‘spot.list.samples’
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.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.htmlSampleSummary: no visible binding for global variable
  ‘spot.list.samples’
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.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: 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 global variable
  ‘indata.original’
pipeline.prepare: no visible binding for '<<-' assignment to
  ‘indata.original’
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 ‘colramp’
pipeline.prepare: no visible binding for '<<-' assignment to ‘colramp’
pipeline.prepare: no visible global function definition for ‘colramp’
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 global variable
  ‘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
  ‘loglog.metadata’
pipeline.prepare: no visible binding for '<<-' assignment to
  ‘WAD.metadata’
pipeline.prepare: no visible binding for '<<-' assignment to
  ‘group.metadata’
pipeline.prepare: no visible binding for '<<-' assignment to
  ‘loglog.group.metadata’
pipeline.prepare: no visible binding for global variable
  ‘loglog.metadata’
pipeline.prepare: no visible binding for '<<-' assignment to
  ‘WAD.group.metadata’
pipeline.prepare: no visible binding for global variable ‘WAD.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.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 : <anonymous>: no visible binding for global
  variable ‘gene.ids’
pipeline.prepareAnnotation: no visible binding for global variable
  ‘opossom.genesets’
pipeline.prepareAnnotation : <anonymous>: no visible binding for global
  variable ‘unique.protein.ids’
pipeline.prepareAnnotation: no visible binding for '<<-' assignment to
  ‘gs.def.list.categories’
pipeline.qualityCheck: no visible binding for global variable
  ‘output.paths’
pipeline.qualityCheck : plot.poly.density: no visible binding for
  global variable ‘indata’
pipeline.qualityCheck: no visible binding for global variable ‘indata’
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
  ‘indata.sample.mean’
pipeline.qualityCheck: no visible binding for global variable
  ‘group.colors’
pipeline.sampleExpressionPortraits: no visible binding for global
  variable ‘files.name’
pipeline.sampleExpressionPortraits: no visible binding for global
  variable ‘group.labels’
pipeline.sampleExpressionPortraits: no visible binding for global
  variable ‘groupwise.group.colors’
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 ‘colramp’
pipeline.sampleExpressionPortraits: no visible binding for global
  variable ‘indata’
pipeline.sampleExpressionPortraits: no visible binding for global
  variable ‘group.silhouette.coef’
pipeline.sampleExpressionPortraits: no visible binding for global
  variable ‘p.m’
pipeline.sampleExpressionPortraits: no visible binding for global
  variable ‘WAD.metadata’
pipeline.sampleExpressionPortraits: no visible binding for global
  variable ‘loglog.metadata’
pipeline.sampleExpressionPortraits: no visible binding for global
  variable ‘t.m’
pipeline.sampleRankMaps: no visible binding for global variable
  ‘files.name’
pipeline.sampleRankMaps: no visible binding for global variable
  ‘group.labels’
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
  ‘colramp’
pipeline.sampleRankMaps: no visible binding for global variable
  ‘WAD.g.m’
pipeline.sampleRankMaps: no visible binding for global variable ‘t.g.m’
pipeline.signatureSets: no visible binding for global variable
  ‘spot.list.overexpression’
pipeline.signatureSets : <anonymous>: no visible binding for global
  variable ‘indata’
pipeline.signatureSets : <anonymous>: no visible binding for global
  variable ‘metadata’
pipeline.signatureSets : <anonymous>: no visible binding for global
  variable ‘som.nodes’
pipeline.signatureSets: no visible binding for global variable
  ‘gene.ids’
pipeline.signatureSets: no visible binding for global variable
  ‘files.name’
pipeline.summarySheetsGroups: no visible binding for global variable
  ‘metadata’
pipeline.summarySheetsGroups: no visible binding for global variable
  ‘group.labels’
pipeline.summarySheetsGroups: no visible binding for global variable
  ‘group.metadata’
pipeline.summarySheetsGroups: no visible binding for global variable
  ‘WAD.group.metadata’
pipeline.summarySheetsGroups: no visible binding for global variable
  ‘loglog.group.metadata’
pipeline.summarySheetsGroups: no visible binding for global variable
  ‘files.name’
pipeline.summarySheetsGroups: no visible binding for global variable
  ‘groupwise.group.colors’
pipeline.summarySheetsGroups: no visible binding for global variable
  ‘preferences’
pipeline.summarySheetsGroups: no visible global function definition for
  ‘colramp’
pipeline.summarySheetsGroups: no visible binding for global variable
  ‘group.silhouette.coef’
pipeline.summarySheetsGroups : <anonymous>: no visible binding for
  global variable ‘group.labels’
pipeline.summarySheetsGroups: no visible binding for global variable
  ‘indata’
pipeline.summarySheetsGroups: no visible binding for global variable
  ‘group.colors’
pipeline.summarySheetsGroups : <anonymous>: no visible binding for
  global variable ‘groupwise.group.colors’
pipeline.summarySheetsIntegral : plot.set.list: no visible binding for
  global variable ‘preferences’
pipeline.summarySheetsIntegral : plot.set.list: no visible global
  function definition for ‘colramp’
pipeline.summarySheetsIntegral : plot.set.list: no visible binding for
  global variable ‘indata’
pipeline.summarySheetsIntegral : plot.set.list: no visible binding for
  global variable ‘metadata’
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 binding for
  global variable ‘spot.list.samples’
pipeline.summarySheetsIntegral : plot.set.list : <anonymous>: no
  visible binding for global variable ‘indata’
pipeline.summarySheetsIntegral : plot.set.list : <anonymous>: no
  visible binding for global variable ‘metadata’
pipeline.summarySheetsIntegral : plot.set.list : <anonymous>: no
  visible binding for global variable ‘som.nodes’
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 binding for
  global variable ‘gs.def.list.categories’
pipeline.summarySheetsIntegral : csv.set.list : <anonymous>: no visible
  binding for global variable ‘indata’
pipeline.summarySheetsIntegral : csv.set.list : <anonymous>: no visible
  binding for global variable ‘metadata’
pipeline.summarySheetsIntegral : csv.set.list : <anonymous>: no visible
  binding for global variable ‘som.nodes’
pipeline.summarySheetsIntegral : csv.set.list: no visible binding for
  global variable ‘indata’
pipeline.summarySheetsIntegral : csv.set.list : <anonymous>: no visible
  binding for global variable ‘sd.g.m’
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.categories’
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 ‘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: no visible binding for global variable
  ‘output.paths’
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
  ‘group.labels’
pipeline.summarySheetsIntegral: no visible binding for global variable
  ‘spot.list.group.overexpression’
pipeline.summarySheetsIntegral: no visible binding for global variable
  ‘preferences’
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 binding for global variable
  ‘p.g.m’
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 binding for global variable
  ‘metadata’
pipeline.summarySheetsSamples: no visible global function definition
  for ‘colramp’
pipeline.summarySheetsSamples: no visible binding for global variable
  ‘spot.list.samples’
pipeline.summarySheetsSamples: no visible binding for global variable
  ‘gene.coordinates’
pipeline.summarySheetsSamples: no visible binding for global variable
  ‘gene.descriptions’
pipeline.summarySheetsSamples: no visible binding for global variable
  ‘n.0.m’
pipeline.summarySheetsSamples: no visible binding for global variable
  ‘Fdr.g.m’
pipeline.summarySheetsSamples: no visible binding for global variable
  ‘gs.def.list.categories’
pipeline.summarySheetsSamples : <anonymous>: no visible binding for
  global variable ‘gene.ids’
pipeline.supportingMaps: no visible binding for global variable
  ‘files.name’
pipeline.supportingMaps: no visible binding for global variable
  ‘som.result’
pipeline.supportingMaps: no visible binding for global variable
  ‘preferences’
pipeline.supportingMaps: no visible global function definition for
  ‘colramp’
pipeline.supportingMaps: no visible binding for global variable
  ‘metadata’
pipeline.supportingMaps: no visible binding for global variable ‘p.m’
pipeline.supportingMaps : <anonymous>: no visible binding for global
  variable ‘indata’
pipeline.supportingMaps: no visible binding for global variable
  ‘som.nodes’
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 binding for global variable
  ‘group.labels’
pipeline.supportingMaps: no visible binding for global variable
  ‘group.colors’
pipeline.topologyProfiles: no visible binding for global variable
  ‘metadata’
pipeline.topologyProfiles: no visible binding for global variable
  ‘loglog.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 binding for global variable
  ‘spot.list.samples’
pipeline.topologyProfiles: no visible binding for global variable
  ‘group.colors’
pipeline.topologyProfiles: no visible binding for global variable
  ‘indata’
pipeline.topologyProfiles: no visible binding for global variable
  ‘groupwise.group.colors’
pipeline.topologyProfiles : <anonymous>: no visible binding for global
  variable ‘group.labels’
pipeline.topologyProfiles: no visible binding for global variable
  ‘preferences’
pipeline.topologyProfiles : <anonymous>: no visible binding for global
  variable ‘som.result’
pipeline.topologyProfiles : <anonymous>: no visible binding for global
  variable ‘preferences’
* 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 ... [58s/143s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
oposSOM-package 36.089  1.228  81.163
opossom.run     12.198  0.546  54.058
* 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-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-package36.089 1.22881.163
opossom.new0.2470.0120.259
opossom.run12.198 0.54654.058