BioC 3.3: CHECK report for oposSOM on moscato2

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### Running command:
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###   rm -rf oposSOM.buildbin-libdir oposSOM.Rcheck && mkdir oposSOM.buildbin-libdir oposSOM.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=oposSOM.buildbin-libdir oposSOM_1.10.0.tar.gz >oposSOM.Rcheck\00install.out 2>&1 && cp oposSOM.Rcheck\00install.out oposSOM-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=oposSOM.buildbin-libdir --install="check:oposSOM-install.out" --force-multiarch --no-vignettes --timings oposSOM_1.10.0.tar.gz
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* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/oposSOM.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'oposSOM/DESCRIPTION' ... OK
* this is package 'oposSOM' version '1.10.0'
* 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 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
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
oposSOM-package 49.06   0.58   85.09
opossom.run     10.57   0.26   40.80
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
oposSOM-package 43.74   0.50   76.68
opossom.run     11.56   0.39   27.35
* 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
  'E:/biocbld/bbs-3.3-bioc/meat/oposSOM.Rcheck/00check.log'
for details.
name	user	system	elapsed
oposSOM-package	49.06	0.58	85.09
opossom.new	0.14	0.01	0.15
opossom.run	10.57	0.26	40.80
BioC 3.3: CHECK report for oposSOM on moscato2

Summary

Command output
