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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:oposSOM.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings oposSOM_2.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/oposSOM.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘oposSOM/DESCRIPTION’ ... OK
* this is package ‘oposSOM’ version ‘2.8.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘oposSOM’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘tools:::makeLazyLoadDB’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... WARNING
sort:
function(x, decreasing, ...)
sort.label:
function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
sort.label
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GeneSet.Fisher : fn: no visible global function definition for
‘fisher.test’
Smooth.Matrix: no visible binding for global variable ‘v’
biomart.available: no visible binding for global variable ‘preferences’
biomart.available: no visible global function definition for ‘is’
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’
modules.CSV.sheets : <anonymous>: no visible binding for global
variable ‘indata’
modules.CSV.sheets : <anonymous>: no visible global function definition
for ‘cor’
modules.CSV.sheets: no visible binding for global variable ‘indata’
modules.CSV.sheets: no visible global function definition for ‘pt’
modules.CSV.sheets: no visible binding for global variable ‘gene.info’
modules.CSV.sheets: no visible binding for global variable
‘indata.gene.mean’
modules.CSV.sheets: no visible binding for global variable ‘sd’
modules.CSV.sheets: no visible global function definition for
‘csv.function’
modules.chromosomes: no visible binding for global variable
‘chromosome.list’
modules.chromosomes: no visible global function definition for ‘pdf’
modules.chromosomes : <anonymous>: no visible binding for global
variable ‘chromosome.list’
modules.chromosomes: no visible global function definition for
‘colorRampPalette’
modules.chromosomes: no visible binding for global variable ‘head’
modules.chromosomes: no visible global function definition for ‘par’
modules.chromosomes: no visible global function definition for ‘image’
modules.chromosomes: no visible global function definition for ‘title’
modules.chromosomes: no visible global function definition for ‘box’
modules.chromosomes: no visible global function definition for ‘abline’
modules.chromosomes: no visible global function definition for ‘axis’
modules.chromosomes: no visible global function definition for ‘layout’
modules.chromosomes: no visible global function definition for ‘text’
modules.chromosomes: no visible global function definition for
‘dev.off’
modules.profiles: no visible global function definition for ‘sd’
modules.profiles: no visible global function definition for ‘pdf’
modules.profiles: no visible global function definition for ‘layout’
modules.profiles: no visible global function definition for ‘par’
modules.profiles: no visible global function definition for ‘image’
modules.profiles: no visible binding for global variable ‘preferences’
modules.profiles: no visible global function definition for ‘axis’
modules.profiles: no visible global function definition for ‘box’
modules.profiles: no visible global function definition for ‘barplot’
modules.profiles: no visible binding for global variable ‘group.colors’
modules.profiles: no visible binding for global variable ‘indata’
modules.profiles: no visible global function definition for ‘abline’
modules.profiles: no visible binding for global variable ‘group.labels’
modules.profiles: no visible global function definition for ‘text’
modules.profiles: no visible binding for global variable
‘groupwise.group.colors’
modules.profiles: no visible global function definition for ‘boxplot’
modules.profiles: no visible global function definition for ‘dev.off’
modules.relations: no visible global function definition for ‘sd’
modules.relations: no visible global function definition for ‘pdf’
modules.relations: no visible global function definition for ‘cor’
modules.relations: no visible global function definition for ‘layout’
modules.relations: no visible global function definition for ‘par’
modules.relations: no visible global function definition for ‘image’
modules.relations: no visible binding for global variable ‘preferences’
modules.relations: no visible global function definition for ‘box’
modules.relations: no visible global function definition for ‘legend’
modules.relations : <anonymous>: no visible binding for global variable
‘group.labels’
modules.relations : <anonymous> : <anonymous>: no visible binding for
global variable ‘group.labels’
modules.relations : <anonymous> : <anonymous>: no visible binding for
global variable ‘indata’
modules.relations: no visible global function definition for
‘graph.empty’
modules.relations: no visible global function definition for
‘add_edges’
modules.relations: no visible binding for global variable
‘groupwise.group.colors’
modules.relations: no visible global function definition for ‘title’
modules.relations: no visible binding for global variable
‘group.labels’
modules.relations: no visible global function definition for ‘frame’
modules.relations: no visible global function definition for ‘text’
modules.relations: no visible global function definition for ‘barplot’
modules.relations: no visible global function definition for ‘dev.off’
modules.report.sheets: no visible global function definition for ‘pdf’
modules.report.sheets: no visible global function definition for
‘layout’
modules.report.sheets: no visible global function definition for ‘par’
modules.report.sheets: no visible global function definition for
‘color.palette.portraits’
modules.report.sheets: no visible global function definition for
‘colorRampPalette’
modules.report.sheets: no visible global function definition for
‘image’
modules.report.sheets: no visible binding for global variable
‘preferences’
modules.report.sheets: no visible global function definition for
‘mtext’
modules.report.sheets: no visible global function definition for ‘box’
modules.report.sheets: no visible global function definition for
‘points’
modules.report.sheets: no visible global function definition for ‘text’
modules.report.sheets : <anonymous>: no visible global function
definition for ‘head’
modules.report.sheets: no visible global function definition for
‘legend’
modules.report.sheets: no visible binding for global variable ‘indata’
modules.report.sheets: no visible global function definition for
‘color.palette.heatmaps’
modules.report.sheets: no visible global function definition for ‘axis’
modules.report.sheets: no visible binding for global variable
‘group.labels’
modules.report.sheets: no visible binding for global variable
‘group.colors’
modules.report.sheets: no visible global function definition for
‘frame’
modules.report.sheets: no visible global function definition for ‘sd’
modules.report.sheets: no visible global function definition for ‘cor’
modules.report.sheets: no visible binding for global variable
‘metadata’
modules.report.sheets: no visible global function definition for
‘barplot’
modules.report.sheets : <anonymous>: no visible binding for global
variable ‘indata’
modules.report.sheets : <anonymous>: no visible global function
definition for ‘cor’
modules.report.sheets: no visible global function definition for ‘rect’
modules.report.sheets: no visible binding for global variable
‘gene.info’
modules.report.sheets: no visible binding for global variable
‘gs.def.list’
modules.report.sheets : <anonymous>: no visible binding for global
variable ‘gene.info’
modules.report.sheets: no visible global function definition for ‘is’
modules.report.sheets: no visible global function definition for ‘hist’
modules.report.sheets: no visible global function definition for
‘abline’
modules.report.sheets: no visible global function definition for
‘lines’
modules.report.sheets: no visible global function definition for
‘dev.off’
newProgressBar : up3: no visible global function definition for
‘flush.console’
newProgressBar : kill: no visible global function definition for
‘flush.console’
opossom.new: no visible binding for global variable ‘write.csv2’
opossom.new: no visible global function definition for ‘modifyList’
opossom.run: no visible global function definition for ‘sessionInfo’
pipeline.affymetrixQualityCheck: no visible binding for global variable
‘indata’
pipeline.affymetrixQualityCheck: no visible global function definition
for ‘par’
pipeline.affymetrixQualityCheck: no visible global function definition
for ‘barplot’
pipeline.affymetrixQualityCheck: no visible binding for global variable
‘group.colors’
pipeline.affymetrixQualityCheck: no visible global function definition
for ‘box’
pipeline.affymetrixQualityCheck: no visible binding for global variable
‘group.labels’
pipeline.affymetrixQualityCheck: no visible global function definition
for ‘boxplot’
pipeline.affymetrixQualityCheck: no visible binding for global variable
‘groupwise.group.colors’
pipeline.affymetrixQualityCheck: no visible global function definition
for ‘axis’
pipeline.affymetrixQualityCheck: no visible global function definition
for ‘abline’
pipeline.affymetrixQualityCheck: no visible global function definition
for ‘lines’
pipeline.calcStatistics: no visible binding for '<<-' assignment to
‘WAD.g.m’
pipeline.calcStatistics: no visible binding for global variable
‘indata’
pipeline.calcStatistics: no visible binding for global variable
‘WAD.g.m’
pipeline.calcStatistics: no visible binding for '<<-' assignment to
‘t.g.m’
pipeline.calcStatistics: no visible binding for '<<-' assignment to
‘p.g.m’
pipeline.calcStatistics: no visible binding for '<<-' assignment to
‘n.0.m’
pipeline.calcStatistics: no visible binding for global variable ‘n.0.m’
pipeline.calcStatistics: no visible binding for '<<-' assignment to
‘perc.DE.m’
pipeline.calcStatistics: no visible binding for global variable
‘perc.DE.m’
pipeline.calcStatistics: no visible binding for '<<-' assignment to
‘fdr.g.m’
pipeline.calcStatistics: no visible binding for '<<-' assignment to
‘Fdr.g.m’
pipeline.calcStatistics: no visible binding for global variable
‘indata.gene.mean’
pipeline.calcStatistics: no visible binding for global variable ‘sd’
pipeline.calcStatistics: no visible binding for global variable ‘t.g.m’
pipeline.calcStatistics: no visible global function definition for ‘is’
pipeline.calcStatistics: no visible binding for global variable ‘p.g.m’
pipeline.calcStatistics: no visible binding for global variable
‘fdr.g.m’
pipeline.calcStatistics: no visible binding for global variable
‘Fdr.g.m’
pipeline.calcStatistics: no visible binding for '<<-' assignment to
‘t.m’
pipeline.calcStatistics: no visible binding for '<<-' assignment to
‘p.m’
pipeline.calcStatistics: no visible binding for global variable
‘preferences’
pipeline.calcStatistics: no visible binding for global variable
‘som.result’
pipeline.calcStatistics: no visible binding for global variable ‘t.m’
pipeline.calcStatistics: no visible global function definition for
‘na.omit’
pipeline.calcStatistics: no visible binding for global variable ‘p.m’
pipeline.cancerHallmarks : <anonymous>: no visible binding for global
variable ‘gs.def.list’
pipeline.cancerHallmarks : <anonymous>: no visible binding for global
variable ‘gene.info’
pipeline.cancerHallmarks: no visible binding for global variable
‘indata’
pipeline.cancerHallmarks : <anonymous>: no visible binding for global
variable ‘unique.protein.ids’
pipeline.cancerHallmarks : <anonymous>: no visible binding for global
variable ‘t.ensID.m’
pipeline.cancerHallmarks: no visible binding for global variable
‘preferences’
pipeline.cancerHallmarks : <anonymous>: no visible global function
definition for ‘na.omit’
pipeline.cancerHallmarks: no visible binding for global variable
‘files.name’
pipeline.cancerHallmarks: no visible global function definition for
‘pdf’
pipeline.cancerHallmarks: no visible global function definition for
‘layout’
pipeline.cancerHallmarks: no visible binding for global variable
‘group.labels’
pipeline.cancerHallmarks: no visible global function definition for
‘par’
pipeline.cancerHallmarks: no visible global function definition for
‘boxplot’
pipeline.cancerHallmarks: no visible binding for global variable
‘groupwise.group.colors’
pipeline.cancerHallmarks: no visible global function definition for
‘abline’
pipeline.cancerHallmarks: no visible binding for global variable
‘som.result’
pipeline.cancerHallmarks: no visible global function definition for
‘color.palette.heatmaps’
pipeline.cancerHallmarks: no visible global function definition for
‘na.omit’
pipeline.cancerHallmarks: no visible global function definition for
‘title’
pipeline.cancerHallmarks: no visible global function definition for
‘box’
pipeline.cancerHallmarks: no visible global function definition for
‘frame’
pipeline.cancerHallmarks: no visible global function definition for
‘legend’
pipeline.cancerHallmarks: no visible global function definition for
‘dev.off’
pipeline.checkInputParameters: no visible binding for global variable
‘env’
pipeline.checkInputParameters : <anonymous>: no visible global function
definition for ‘is’
pipeline.checkInputParameters : <anonymous>: no visible binding for
global variable ‘indata’
pipeline.checkInputParameters : <anonymous> : <anonymous>: no visible
global function definition for ‘na.omit’
pipeline.checkInputParameters: no visible binding for global variable
‘indata’
pipeline.checkInputParameters: no visible global function definition
for ‘is’
pipeline.checkInputParameters: no visible binding for '<<-' assignment
to ‘group.labels’
pipeline.checkInputParameters: no visible binding for '<<-' assignment
to ‘group.colors’
pipeline.checkInputParameters: no visible binding for '<<-' assignment
to ‘indata’
pipeline.checkInputParameters: no visible binding for global variable
‘group.labels’
pipeline.checkInputParameters: no visible binding for global variable
‘group.colors’
pipeline.checkInputParameters: no visible global function definition
for ‘colorRampPalette’
pipeline.checkInputParameters: no visible global function definition
for ‘col2rgb’
pipeline.checkInputParameters : <anonymous>: no visible global function
definition for ‘rgb’
pipeline.checkInputParameters: no visible binding for '<<-' assignment
to ‘groupwise.group.colors’
pipeline.checkInputParameters: no visible binding for global variable
‘groupwise.group.colors’
pipeline.checkInputParameters: no visible binding for global variable
‘color.palette.portraits’
pipeline.checkInputParameters: no visible binding for '<<-' assignment
to ‘color.palette.portraits’
pipeline.checkInputParameters: no visible binding for global variable
‘color.palette.heatmaps’
pipeline.checkInputParameters: no visible binding for '<<-' assignment
to ‘color.palette.heatmaps’
pipeline.checkInputParameters: no visible binding for '<<-' assignment
to ‘files.name’
pipeline.checkInputParameters: no visible binding for global variable
‘files.name’
pipeline.checkInputParameters: no visible binding for '<<-' assignment
to ‘output.paths’
pipeline.checkInputParameters: no visible global function definition
for ‘sessionInfo’
pipeline.checkInputParameters: no visible binding for '<<-' assignment
to ‘csv.function’
pipeline.checkInputParameters: no visible binding for global variable
‘write.csv’
pipeline.chromosomeExpressionReports: no visible binding for global
variable ‘chromosome.list’
pipeline.chromosomeExpressionReports : <anonymous>: no visible binding
for global variable ‘gene.info’
pipeline.chromosomeExpressionReports: no visible binding for global
variable ‘indata’
pipeline.chromosomeExpressionReports : <anonymous>: no visible binding
for global variable ‘indata’
pipeline.chromosomeExpressionReports: no visible global function
definition for ‘hclust’
pipeline.chromosomeExpressionReports: no visible global function
definition for ‘dist’
pipeline.chromosomeExpressionReports: no visible binding for global
variable ‘files.name’
pipeline.chromosomeExpressionReports: no visible global function
definition for ‘pdf’
pipeline.chromosomeExpressionReports: no visible global function
definition for ‘layout’
pipeline.chromosomeExpressionReports: no visible global function
definition for ‘par’
pipeline.chromosomeExpressionReports: no visible global function
definition for ‘image’
pipeline.chromosomeExpressionReports: no visible global function
definition for ‘color.palette.heatmaps’
pipeline.chromosomeExpressionReports: no visible global function
definition for ‘box’
pipeline.chromosomeExpressionReports: no visible global function
definition for ‘abline’
pipeline.chromosomeExpressionReports: no visible global function
definition for ‘axis’
pipeline.chromosomeExpressionReports: no visible binding for global
variable ‘group.colors’
pipeline.chromosomeExpressionReports: no visible global function
definition for ‘dev.off’
pipeline.detectEnsemblDataset: no visible binding for '<<-' assignment
to ‘preferences’
pipeline.detectEnsemblDataset: no visible binding for global variable
‘preferences’
pipeline.detectEnsemblDataset: no visible binding for global variable
‘indata’
pipeline.detectSpotsIntegral: no visible binding for global variable
‘metadata’
pipeline.detectSpotsIntegral: no visible binding for global variable
‘indata’
pipeline.detectSpotsIntegral: no visible binding for global variable
‘preferences’
pipeline.detectSpotsIntegral: no visible binding for '<<-' assignment
to ‘spot.list.overexpression’
pipeline.detectSpotsIntegral: no visible binding for global variable
‘spot.list.overexpression’
pipeline.detectSpotsIntegral: no visible binding for global variable
‘som.result’
pipeline.detectSpotsIntegral : <anonymous>: no visible binding for
global variable ‘metadata’
pipeline.detectSpotsIntegral : <anonymous>: no visible binding for
global variable ‘indata’
pipeline.detectSpotsIntegral: no visible binding for '<<-' assignment
to ‘spot.list.underexpression’
pipeline.detectSpotsIntegral: no visible binding for global variable
‘spot.list.underexpression’
pipeline.detectSpotsIntegral: no visible binding for '<<-' assignment
to ‘spot.list.correlation’
pipeline.detectSpotsIntegral: no visible binding for global variable
‘spot.list.correlation’
pipeline.detectSpotsIntegral: no visible global function definition for
‘cor’
pipeline.detectSpotsIntegral: no visible global function definition for
‘kmeans’
pipeline.detectSpotsIntegral: no visible binding for '<<-' assignment
to ‘spot.list.kmeans’
pipeline.detectSpotsIntegral: no visible binding for global variable
‘spot.list.kmeans’
pipeline.detectSpotsIntegral: no visible binding for global variable
‘group.labels’
pipeline.detectSpotsIntegral: no visible binding for '<<-' assignment
to ‘spot.list.group.overexpression’
pipeline.detectSpotsIntegral: no visible binding for global variable
‘spot.list.group.overexpression’
pipeline.detectSpotsIntegral : <anonymous>: no visible binding for
global variable ‘preferences’
pipeline.detectSpotsIntegral : <anonymous>: no visible global function
definition for ‘dist’
pipeline.detectSpotsIntegral: no visible binding for '<<-' assignment
to ‘spot.list.dmap’
pipeline.detectSpotsIntegral: no visible binding for global variable
‘spot.list.dmap’
pipeline.detectSpotsIntegral: no visible global function definition for
‘na.omit’
pipeline.detectSpotsIntegral : <anonymous>: no visible global function
definition for ‘sd’
pipeline.detectSpotsIntegral : <anonymous>: no visible binding for
global variable ‘spot.list.dmap’
pipeline.detectSpotsIntegral: no visible binding for '<<-' assignment
to ‘preferences’
pipeline.detectSpotsSamples: no visible binding for '<<-' assignment to
‘spot.list.samples’
pipeline.detectSpotsSamples: no visible binding for global variable
‘indata’
pipeline.detectSpotsSamples: no visible binding for global variable
‘spot.list.samples’
pipeline.differenceAnalyses: no visible global function definition for
‘combn’
pipeline.differenceAnalyses: no visible binding for global variable
‘files.name’
pipeline.differenceAnalyses: no visible binding for global variable
‘var’
pipeline.differenceAnalyses: no visible global function definition for
‘pt’
pipeline.differenceAnalyses: no visible global function definition for
‘is’
pipeline.entropyProfiles: no visible binding for global variable
‘files.name’
pipeline.entropyProfiles: no visible global function definition for
‘pdf’
pipeline.entropyProfiles: no visible global function definition for
‘par’
pipeline.entropyProfiles: no visible global function definition for
‘barplot’
pipeline.entropyProfiles: no visible binding for global variable
‘metadata’
pipeline.entropyProfiles: no visible binding for global variable
‘group.colors’
pipeline.entropyProfiles: no visible binding for global variable
‘indata’
pipeline.entropyProfiles: no visible global function definition for
‘box’
pipeline.entropyProfiles: no visible binding for global variable
‘group.labels’
pipeline.entropyProfiles: no visible global function definition for
‘boxplot’
pipeline.entropyProfiles: no visible binding for global variable
‘groupwise.group.colors’
pipeline.entropyProfiles: no visible global function definition for
‘axis’
pipeline.entropyProfiles: no visible binding for global variable ‘var’
pipeline.entropyProfiles: no visible global function definition for
‘quantile’
pipeline.entropyProfiles : <anonymous>: no visible global function
definition for ‘hist’
pipeline.entropyProfiles : <anonymous>: no visible binding for global
variable ‘preferences’
pipeline.entropyProfiles: no visible binding for global variable
‘som.result’
pipeline.entropyProfiles: no visible global function definition for
‘dev.off’
pipeline.geneLists: no visible binding for global variable ‘som.result’
pipeline.geneLists: no visible binding for global variable ‘indata’
pipeline.geneLists: no visible binding for global variable ‘gene.info’
pipeline.geneLists: no visible binding for global variable
‘indata.gene.mean’
pipeline.geneLists: no visible binding for global variable ‘files.name’
pipeline.geneLists: no visible global function definition for
‘csv.function’
pipeline.geneLists: no visible binding for global variable
‘output.paths’
pipeline.geneLists: no visible binding for global variable
‘samples.GSZ.scores’
pipeline.geneLists: no visible binding for global variable
‘preferences’
pipeline.geneLists: no visible binding for global variable ‘p.g.m’
pipeline.geneLists: no visible binding for global variable ‘WAD.g.m’
pipeline.geneLists: no visible binding for global variable ‘t.g.m’
pipeline.geneLists: no visible binding for global variable ‘fdr.g.m’
pipeline.geneLists: no visible binding for global variable ‘Fdr.g.m’
pipeline.geneLists: no visible binding for global variable ‘perc.DE.m’
pipeline.geneLists: no visible binding for global variable
‘spot.list.samples’
pipeline.generateSOM: no visible binding for '<<-' assignment to
‘som.result’
pipeline.generateSOM: no visible binding for global variable ‘indata’
pipeline.generateSOM: no visible binding for global variable
‘preferences’
pipeline.generateSOM: no visible binding for global variable
‘som.result’
pipeline.generateSOM: no visible binding for '<<-' assignment to
‘metadata’
pipeline.generateSOM: no visible binding for global variable ‘metadata’
pipeline.generateSOM: no visible binding for '<<-' assignment to
‘gene.info’
pipeline.generateSOM: no visible binding for global variable
‘gene.info’
pipeline.genesetOverviews: no visible binding for global variable
‘files.name’
pipeline.genesetOverviews: no visible global function definition for
‘pdf’
pipeline.genesetOverviews: no visible binding for global variable
‘preferences’
pipeline.genesetOverviews : <anonymous>: no visible binding for global
variable ‘gs.def.list’
pipeline.genesetOverviews: no visible binding for global variable
‘gs.def.list’
pipeline.genesetOverviews: no visible binding for global variable
‘samples.GSZ.scores’
pipeline.genesetOverviews: no visible binding for global variable
‘indata’
pipeline.genesetOverviews: no visible global function definition for
‘quantile’
pipeline.genesetOverviews: no visible global function definition for
‘color.palette.heatmaps’
pipeline.genesetOverviews: no visible binding for global variable
‘group.colors’
pipeline.genesetOverviews: no visible global function definition for
‘par’
pipeline.genesetOverviews: no visible global function definition for
‘image’
pipeline.genesetOverviews: no visible global function definition for
‘box’
pipeline.genesetOverviews: no visible global function definition for
‘axis’
pipeline.genesetOverviews: no visible global function definition for
‘mtext’
pipeline.genesetOverviews: no visible binding for global variable
‘group.labels’
pipeline.genesetOverviews : <anonymous>: no visible binding for global
variable ‘group.labels’
pipeline.genesetOverviews : <anonymous>: no visible global function
definition for ‘hclust’
pipeline.genesetOverviews : <anonymous>: no visible global function
definition for ‘dist’
pipeline.genesetOverviews: no visible binding for global variable
‘spot.list.samples’
pipeline.genesetOverviews: no visible global function definition for
‘hist’
pipeline.genesetOverviews: no visible global function definition for
‘abline’
pipeline.genesetOverviews: no visible global function definition for
‘lines’
pipeline.genesetOverviews: no visible global function definition for
‘legend’
pipeline.genesetOverviews: no visible global function definition for
‘dev.off’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
‘files.name’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
‘samples.GSZ.scores’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘quantile’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘sd’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
‘gs.def.list’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘pdf’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘layout’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
‘indata’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
‘gene.info’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
‘sd’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘hclust’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘dist’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘par’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘barplot’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
‘group.colors’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘abline’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘axis’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘mtext’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘frame’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘legend’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
‘groupwise.group.colors’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘image’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘box’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘color.palette.heatmaps’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
‘preferences’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
‘som.result’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘na.omit’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘title’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
‘group.labels’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘boxplot’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘dev.off’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘csv.function’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘setTxtProgressBar’
pipeline.genesetStatisticIntegral : spot.fisher.p: no visible global
function definition for ‘na.omit’
pipeline.genesetStatisticIntegral : spot.fisher.p: no visible binding
for global variable ‘gene.info’
pipeline.genesetStatisticIntegral : spot.fisher.p: no visible binding
for global variable ‘unique.protein.ids’
pipeline.genesetStatisticIntegral : spot.fisher.p: no visible binding
for global variable ‘gs.def.list’
pipeline.genesetStatisticIntegral: no visible binding for '<<-'
assignment to ‘spot.list.overexpression’
pipeline.genesetStatisticIntegral: no visible binding for global
variable ‘spot.list.overexpression’
pipeline.genesetStatisticIntegral: no visible binding for '<<-'
assignment to ‘spot.list.underexpression’
pipeline.genesetStatisticIntegral: no visible binding for global
variable ‘spot.list.underexpression’
pipeline.genesetStatisticIntegral: no visible binding for global
variable ‘spot.list.correlation’
pipeline.genesetStatisticIntegral: no visible binding for '<<-'
assignment to ‘spot.list.correlation’
pipeline.genesetStatisticIntegral: no visible binding for '<<-'
assignment to ‘spot.list.kmeans’
pipeline.genesetStatisticIntegral: no visible binding for global
variable ‘spot.list.kmeans’
pipeline.genesetStatisticIntegral: no visible binding for global
variable ‘group.labels’
pipeline.genesetStatisticIntegral: no visible binding for '<<-'
assignment to ‘spot.list.group.overexpression’
pipeline.genesetStatisticIntegral: no visible binding for global
variable ‘spot.list.group.overexpression’
pipeline.genesetStatisticIntegral: no visible binding for '<<-'
assignment to ‘spot.list.dmap’
pipeline.genesetStatisticIntegral: no visible binding for global
variable ‘spot.list.dmap’
pipeline.genesetStatisticSamples: no visible binding for '<<-'
assignment to ‘t.ensID.m’
pipeline.genesetStatisticSamples: no visible binding for global
variable ‘t.g.m’
pipeline.genesetStatisticSamples: no visible binding for global
variable ‘indata’
pipeline.genesetStatisticSamples: no visible binding for global
variable ‘gene.info’
pipeline.genesetStatisticSamples: no visible binding for global
variable ‘t.ensID.m’
pipeline.genesetStatisticSamples: no visible binding for global
variable ‘preferences’
pipeline.genesetStatisticSamples: no visible binding for global
variable ‘gs.def.list’
pipeline.genesetStatisticSamples: no visible binding for global
variable ‘unique.protein.ids’
pipeline.genesetStatisticSamples : <anonymous>: no visible binding for
global variable ‘t.ensID.m’
pipeline.genesetStatisticSamples : <anonymous>: no visible binding for
global variable ‘unique.protein.ids’
pipeline.genesetStatisticSamples: no visible global function definition
for ‘ecdf’
pipeline.genesetStatisticSamples: no visible binding for '<<-'
assignment to ‘spot.list.samples’
pipeline.genesetStatisticSamples: no visible binding for global
variable ‘spot.list.samples’
pipeline.genesetStatisticSamples : <anonymous>: no visible binding for
global variable ‘spot.list.samples’
pipeline.genesetStatisticSamples : <anonymous>: no visible binding for
global variable ‘gs.def.list’
pipeline.genesetStatisticSamples : <anonymous>: no visible binding for
global variable ‘preferences’
pipeline.genesetStatisticSamples: no visible binding for '<<-'
assignment to ‘samples.GSZ.scores’
pipeline.groupAnalysis: no visible binding for global variable
‘files.name’
pipeline.groupAnalysis : <anonymous>: no visible global function
definition for ‘sd’
pipeline.groupAnalysis: no visible global function definition for ‘pt’
pipeline.groupAnalysis: no visible global function definition for ‘is’
pipeline.groupAssignment: no visible binding for global variable
‘group.labels’
pipeline.groupAssignment: no visible binding for global variable
‘pat.labels’
pipeline.groupAssignment: no visible binding for global variable
‘preferences’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
‘group.labels’
pipeline.groupAssignment: no visible binding for global variable
‘indata’
pipeline.groupAssignment: no visible binding for global variable
‘files.name’
pipeline.groupAssignment: no visible global function definition for
‘pdf’
pipeline.groupAssignment: no visible global function definition for
‘barplot’
pipeline.groupAssignment: no visible global function definition for
‘box’
pipeline.groupAssignment: no visible global function definition for
‘lines’
pipeline.groupAssignment: no visible global function definition for
‘abline’
pipeline.groupAssignment: no visible global function definition for
‘dev.off’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
‘pat.labels’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
‘group.colors’
pipeline.groupAssignment: no visible binding for global variable
‘group.colors’
pipeline.groupAssignment: no visible global function definition for
‘colorRampPalette’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
‘groupwise.group.colors’
pipeline.groupAssignment: no visible binding for global variable
‘groupwise.group.colors’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
‘t.g.m’
pipeline.groupAssignment: no visible binding for global variable
‘t.g.m’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
‘p.g.m’
pipeline.groupAssignment: no visible binding for global variable
‘p.g.m’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
‘fdr.g.m’
pipeline.groupAssignment: no visible binding for global variable
‘fdr.g.m’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
‘Fdr.g.m’
pipeline.groupAssignment: no visible binding for global variable
‘Fdr.g.m’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
‘WAD.g.m’
pipeline.groupAssignment: no visible binding for global variable
‘WAD.g.m’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
‘n.0.m’
pipeline.groupAssignment: no visible binding for global variable
‘n.0.m’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
‘perc.DE.m’
pipeline.groupAssignment: no visible binding for global variable
‘perc.DE.m’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
‘t.m’
pipeline.groupAssignment: no visible binding for global variable ‘t.m’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
‘p.m’
pipeline.groupAssignment: no visible binding for global variable ‘p.m’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
‘indata’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
‘metadata’
pipeline.groupAssignment: no visible binding for global variable
‘metadata’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
‘indata.sample.mean’
pipeline.groupAssignment: no visible binding for global variable
‘indata.sample.mean’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
‘spot.list.samples’
pipeline.groupAssignment: no visible binding for global variable
‘spot.list.samples’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
‘group.silhouette.coef’
pipeline.groupAssignment: no visible global function definition for
‘cor’
pipeline.groupAssignment : <anonymous>: no visible binding for global
variable ‘group.labels’
pipeline.groupAssignment: no visible binding for global variable
‘group.silhouette.coef’
pipeline.groupSpecificGenesets: no visible global function definition
for ‘sd’
pipeline.groupSpecificGenesets: no visible binding for global variable
‘samples.GSZ.scores’
pipeline.groupSpecificGenesets: no visible binding for global variable
‘group.labels’
pipeline.groupSpecificGenesets : <anonymous>: no visible global
function definition for ‘wilcox.test’
pipeline.groupSpecificGenesets : <anonymous>: no visible binding for
global variable ‘group.labels’
pipeline.groupSpecificGenesets: no visible global function definition
for ‘pdf’
pipeline.groupSpecificGenesets: no visible binding for global variable
‘files.name’
pipeline.groupSpecificGenesets: no visible global function definition
for ‘layout’
pipeline.groupSpecificGenesets: no visible global function definition
for ‘par’
pipeline.groupSpecificGenesets: no visible global function definition
for ‘barplot’
pipeline.groupSpecificGenesets: no visible binding for global variable
‘group.colors’
pipeline.groupSpecificGenesets: no visible binding for global variable
‘indata’
pipeline.groupSpecificGenesets: no visible global function definition
for ‘abline’
pipeline.groupSpecificGenesets: no visible global function definition
for ‘title’
pipeline.groupSpecificGenesets: no visible global function definition
for ‘mtext’
pipeline.groupSpecificGenesets: no visible binding for global variable
‘preferences’
pipeline.groupSpecificGenesets: no visible binding for global variable
‘som.result’
pipeline.groupSpecificGenesets: no visible binding for global variable
‘gene.info’
pipeline.groupSpecificGenesets: no visible binding for global variable
‘gs.def.list’
pipeline.groupSpecificGenesets: no visible global function definition
for ‘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 ‘csv.function’
pipeline.groupSpecificGenesets : <anonymous>: no visible global
function definition for ‘aov’
pipeline.groupSpecificGenesets: no visible global function definition
for ‘text’
pipeline.groupSpecificGenesets: no visible binding for global variable
‘groupwise.group.colors’
pipeline.htmlDifferencesSummary: no visible binding for global variable
‘files.name’
pipeline.htmlDifferencesSummary: no visible binding for global variable
‘indata’
pipeline.htmlGenesetAnalysis: no visible binding for global variable
‘preferences’
pipeline.htmlGenesetAnalysis: no visible binding for global variable
‘files.name’
pipeline.htmlGenesetAnalysis: no visible binding for global variable
‘gs.def.list’
pipeline.htmlGroupSummary: no visible binding for global variable
‘group.labels’
pipeline.htmlGroupSummary: no visible binding for global variable
‘files.name’
pipeline.htmlGroupSummary: no visible binding for global variable
‘preferences’
pipeline.htmlGroupSummary: no visible binding for global variable
‘indata’
pipeline.htmlModuleSummary: no visible binding for global variable
‘files.name’
pipeline.htmlModuleSummary: no visible binding for global variable
‘group.labels’
pipeline.htmlModuleSummary: no visible binding for global variable
‘spot.list.overexpression’
pipeline.htmlModuleSummary: no visible binding for global variable
‘spot.list.group.overexpression’
pipeline.htmlModuleSummary: no visible binding for global variable
‘spot.list.kmeans’
pipeline.htmlModuleSummary: no visible binding for global variable
‘spot.list.dmap’
pipeline.htmlSampleSummary: no visible binding for global variable
‘indata’
pipeline.htmlSampleSummary: no visible binding for global variable
‘files.name’
pipeline.htmlSampleSummary: no visible binding for global variable
‘group.labels’
pipeline.htmlSummary: no visible binding for global variable
‘files.name’
pipeline.htmlSummary: no visible binding for global variable
‘preferences’
pipeline.htmlSummary: no visible binding for global variable ‘indata’
pipeline.htmlSummary: no visible binding for global variable
‘group.labels’
pipeline.moduleCorrelationMap: no visible global function definition
for ‘quantile’
pipeline.moduleCorrelationMap: no visible global function definition
for ‘layout’
pipeline.moduleCorrelationMap: no visible global function definition
for ‘par’
pipeline.moduleCorrelationMap: no visible global function definition
for ‘image’
pipeline.moduleCorrelationMap: no visible binding for global variable
‘group.colors’
pipeline.moduleCorrelationMap: no visible global function definition
for ‘color.palette.heatmaps’
pipeline.moduleCorrelationMap: no visible global function definition
for ‘box’
pipeline.moduleCorrelationMap : <anonymous>: no visible global function
definition for ‘rect’
pipeline.moduleCorrelationMap: no visible binding for global variable
‘preferences’
pipeline.moduleCorrelationMap : <anonymous>: no visible global function
definition for ‘sd’
pipeline.moduleCorrelationMap : <anonymous>: no visible global function
definition for ‘text’
pipeline.moduleCorrelationMap: no visible global function definition
for ‘as.dendrogram’
pipeline.moduleCorrelationMap: no visible global function definition
for ‘title’
pipeline.patAssignment: no visible binding for global variable
‘preferences’
pipeline.patAssignment: no visible global function definition for ‘sd’
pipeline.patAssignment: no visible binding for '<<-' assignment to
‘pat.labels’
pipeline.patAssignment: no visible binding for global variable
‘pat.labels’
pipeline.prepareAnnotation: no visible binding for global variable
‘indata’
pipeline.prepareAnnotation: no visible binding for '<<-' assignment to
‘gene.info’
pipeline.prepareAnnotation: no visible binding for global variable
‘preferences’
pipeline.prepareAnnotation: no visible binding for global variable
‘gene.info’
pipeline.prepareAnnotation: no visible binding for global variable
‘som.result’
pipeline.prepareAnnotation: no visible binding for '<<-' assignment to
‘chromosome.list’
pipeline.prepareAnnotation: no visible binding for '<<-' assignment to
‘preferences’
pipeline.prepareAnnotation: no visible binding for global variable
‘chromosome.list’
pipeline.prepareAnnotation: no visible binding for '<<-' assignment to
‘unique.protein.ids’
pipeline.prepareAnnotation: no visible binding for global variable
‘unique.protein.ids’
pipeline.prepareAnnotation: no visible binding for '<<-' assignment to
‘gs.def.list’
pipeline.prepareAnnotation: no visible binding for global variable
‘gs.def.list’
pipeline.prepareAnnotation: no visible binding for global variable
‘head’
pipeline.prepareAnnotation : <anonymous>: no visible binding for global
variable ‘gene.info’
pipeline.prepareAnnotation: no visible global function definition for
‘data’
pipeline.prepareAnnotation: no visible binding for global variable
‘opossom.genesets’
pipeline.prepareAnnotation : <anonymous>: no visible binding for global
variable ‘unique.protein.ids’
pipeline.prepareIndata: no visible binding for '<<-' assignment to
‘indata.sample.mean’
pipeline.prepareIndata: no visible binding for global variable ‘indata’
pipeline.prepareIndata: no visible binding for global variable
‘preferences’
pipeline.prepareIndata: no visible binding for '<<-' assignment to
‘indata’
pipeline.prepareIndata: no visible binding for '<<-' assignment to
‘group.labels’
pipeline.prepareIndata: no visible binding for global variable
‘group.labels’
pipeline.prepareIndata: no visible binding for '<<-' assignment to
‘group.colors’
pipeline.prepareIndata: no visible binding for global variable
‘group.colors’
pipeline.prepareIndata: no visible binding for '<<-' assignment to
‘indata.gene.mean’
pipeline.prepareIndata: no visible binding for global variable
‘indata.gene.mean’
pipeline.qualityCheck: no visible binding for global variable
‘files.name’
pipeline.qualityCheck : plot.poly.density: no visible binding for
global variable ‘indata’
pipeline.qualityCheck : plot.poly.density: no visible global function
definition for ‘par’
pipeline.qualityCheck : plot.poly.density: no visible global function
definition for ‘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
‘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.sampleSimilarityAnalysisCor : mixColors: no visible binding
for global variable ‘rgb’
pipeline.sampleSimilarityAnalysisCor: no visible global function
definition for ‘col2rgb’
pipeline.sampleSimilarityAnalysisCor: no visible binding for global
variable ‘groupwise.group.colors’
pipeline.sampleSimilarityAnalysisCor : <anonymous>: no visible global
function definition for ‘rgb’
pipeline.sampleSimilarityAnalysisCor: no visible binding for global
variable ‘group.colors’
pipeline.sampleSimilarityAnalysisCor: no visible binding for global
variable ‘group.silhouette.coef’
pipeline.sampleSimilarityAnalysisCor: no visible binding for global
variable ‘group.labels’
pipeline.sampleSimilarityAnalysisCor: no visible global function
definition for ‘cor’
pipeline.sampleSimilarityAnalysisCor: no visible binding for global
variable ‘preferences’
pipeline.sampleSimilarityAnalysisCor: no visible binding for global
variable ‘metadata’
pipeline.sampleSimilarityAnalysisCor: no visible binding for global
variable ‘files.name’
pipeline.sampleSimilarityAnalysisCor: no visible global function
definition for ‘pdf’
pipeline.sampleSimilarityAnalysisCor: no visible global function
definition for ‘par’
pipeline.sampleSimilarityAnalysisCor: no visible global function
definition for ‘get.edgelist’
pipeline.sampleSimilarityAnalysisCor : <anonymous>: no visible binding
for global variable ‘group.colors’
pipeline.sampleSimilarityAnalysisCor: no visible global function
definition for ‘legend’
pipeline.sampleSimilarityAnalysisCor: no visible global function
definition for ‘box’
pipeline.sampleSimilarityAnalysisCor: no visible global function
definition for ‘dev.off’
pipeline.sampleSimilarityAnalysisCor: no visible global function
definition for ‘hclust’
pipeline.sampleSimilarityAnalysisCor: no visible global function
definition for ‘dist’
pipeline.sampleSimilarityAnalysisCor: no visible global function
definition for ‘color.palette.heatmaps’
pipeline.sampleSimilarityAnalysisCor: no visible global function
definition for ‘image’
pipeline.sampleSimilarityAnalysisCor: no visible global function
definition for ‘axis’
pipeline.sampleSimilarityAnalysisCor : <anonymous>: no visible binding
for global variable ‘group.labels’
pipeline.sampleSimilarityAnalysisCor : <anonymous>: no visible global
function definition for ‘hclust’
pipeline.sampleSimilarityAnalysisCor : <anonymous>: no visible global
function definition for ‘dist’
pipeline.sampleSimilarityAnalysisCor: no visible global function
definition for ‘as.dendrogram’
pipeline.sampleSimilarityAnalysisED: no visible binding for global
variable ‘files.name’
pipeline.sampleSimilarityAnalysisED: no visible global function
definition for ‘pdf’
pipeline.sampleSimilarityAnalysisED: no visible binding for global
variable ‘preferences’
pipeline.sampleSimilarityAnalysisED: no visible binding for global
variable ‘metadata’
pipeline.sampleSimilarityAnalysisED: no visible global function
definition for ‘par’
pipeline.sampleSimilarityAnalysisED: no visible binding for global
variable ‘group.colors’
pipeline.sampleSimilarityAnalysisED: no visible global function
definition for ‘title’
pipeline.sampleSimilarityAnalysisED: no visible global function
definition for ‘legend’
pipeline.sampleSimilarityAnalysisED: no visible binding for global
variable ‘group.labels’
pipeline.sampleSimilarityAnalysisED: no visible binding for global
variable ‘groupwise.group.colors’
pipeline.sampleSimilarityAnalysisED: no visible global function
definition for ‘dev.off’
pipeline.sampleSimilarityAnalysisED: no visible global function
definition for ‘dist’
pipeline.sampleSimilarityAnalysisED: no visible global function
definition for ‘box’
pipeline.sampleSimilarityAnalysisED: no visible global function
definition for ‘color.palette.heatmaps’
pipeline.sampleSimilarityAnalysisED: no visible global function
definition for ‘image’
pipeline.sampleSimilarityAnalysisED: no visible global function
definition for ‘axis’
pipeline.sampleSimilarityAnalysisICA: no visible binding for global
variable ‘files.name’
pipeline.sampleSimilarityAnalysisICA: no visible global function
definition for ‘pdf’
pipeline.sampleSimilarityAnalysisICA: no visible binding for global
variable ‘preferences’
pipeline.sampleSimilarityAnalysisICA: no visible binding for global
variable ‘metadata’
pipeline.sampleSimilarityAnalysisICA: no visible global function
definition for ‘layout’
pipeline.sampleSimilarityAnalysisICA: no visible global function
definition for ‘par’
pipeline.sampleSimilarityAnalysisICA: no visible binding for global
variable ‘group.colors’
pipeline.sampleSimilarityAnalysisICA: no visible global function
definition for ‘text’
pipeline.sampleSimilarityAnalysisICA: no visible global function
definition for ‘mtext’
pipeline.sampleSimilarityAnalysisICA: no visible global function
definition for ‘legend’
pipeline.sampleSimilarityAnalysisICA: no visible binding for global
variable ‘group.labels’
pipeline.sampleSimilarityAnalysisICA: no visible binding for global
variable ‘groupwise.group.colors’
pipeline.sampleSimilarityAnalysisICA: no visible global function
definition for ‘points’
pipeline.sampleSimilarityAnalysisICA: no visible global function
definition for ‘box’
pipeline.sampleSimilarityAnalysisICA: no visible binding for global
variable ‘indata’
pipeline.sampleSimilarityAnalysisICA: no visible global function
definition for ‘dev.off’
pipeline.sampleSimilarityAnalysisSOM: no visible binding for global
variable ‘files.name’
pipeline.sampleSimilarityAnalysisSOM: no visible global function
definition for ‘pdf’
pipeline.sampleSimilarityAnalysisSOM: no visible binding for global
variable ‘preferences’
pipeline.sampleSimilarityAnalysisSOM: no visible binding for global
variable ‘metadata’
pipeline.sampleSimilarityAnalysisSOM: no visible global function
definition for ‘par’
pipeline.sampleSimilarityAnalysisSOM: no visible binding for global
variable ‘group.labels’
pipeline.sampleSimilarityAnalysisSOM: no visible global function
definition for ‘legend’
pipeline.sampleSimilarityAnalysisSOM: no visible binding for global
variable ‘groupwise.group.colors’
pipeline.sampleSimilarityAnalysisSOM: no visible global function
definition for ‘points’
pipeline.sampleSimilarityAnalysisSOM: no visible binding for global
variable ‘group.colors’
pipeline.sampleSimilarityAnalysisSOM: no visible global function
definition for ‘box’
pipeline.sampleSimilarityAnalysisSOM: no visible global function
definition for ‘text’
pipeline.sampleSimilarityAnalysisSOM: no visible binding for global
variable ‘indata’
pipeline.sampleSimilarityAnalysisSOM: no visible global function
definition for ‘chull’
pipeline.sampleSimilarityAnalysisSOM: no visible global function
definition for ‘polygon’
pipeline.sampleSimilarityAnalysisSOM: no visible global function
definition for ‘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.summarySheetsModules: no visible binding for global variable
‘files.name’
pipeline.summarySheetsModules: no visible binding for global variable
‘spot.list.overexpression’
pipeline.summarySheetsModules: no visible binding for global variable
‘spot.list.underexpression’
pipeline.summarySheetsModules: no visible binding for global variable
‘spot.list.correlation’
pipeline.summarySheetsModules: no visible binding for global variable
‘spot.list.kmeans’
pipeline.summarySheetsModules: no visible binding for global variable
‘spot.list.dmap’
pipeline.summarySheetsModules: no visible binding for global variable
‘group.labels’
pipeline.summarySheetsModules: no visible binding for global variable
‘spot.list.group.overexpression’
pipeline.summarySheetsModules: no visible binding for global variable
‘output.paths’
pipeline.summarySheetsPATs: no visible binding for global variable
‘files.name’
pipeline.summarySheetsPATs: no visible binding for global variable
‘metadata’
pipeline.summarySheetsPATs: no visible binding for global variable
‘pat.labels’
pipeline.summarySheetsPATs: no visible global function definition for
‘pdf’
pipeline.summarySheetsPATs: no visible global function definition for
‘layout’
pipeline.summarySheetsPATs: no visible global function definition for
‘par’
pipeline.summarySheetsPATs: no visible global function definition for
‘frame’
pipeline.summarySheetsPATs: no visible global function definition for
‘text’
pipeline.summarySheetsPATs: no visible global function definition for
‘image’
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
‘box’
pipeline.summarySheetsPATs: no visible binding for global variable
‘group.labels’
pipeline.summarySheetsPATs: no visible global function definition for
‘pie’
pipeline.summarySheetsPATs: no visible binding for global variable
‘groupwise.group.colors’
pipeline.summarySheetsPATs: no visible global function definition for
‘mtext’
pipeline.summarySheetsPATs : <anonymous>: no visible binding for global
variable ‘group.labels’
pipeline.summarySheetsPATs: no visible global function definition for
‘barplot’
pipeline.summarySheetsPATs: no visible global function definition for
‘legend’
pipeline.summarySheetsPATs : <anonymous>: no visible binding for global
variable ‘pat.labels’
pipeline.summarySheetsPATs: no visible global function definition for
‘dev.off’
pipeline.summarySheetsSamples: no visible binding for global variable
‘indata’
pipeline.summarySheetsSamples: no visible binding for global variable
‘output.paths’
pipeline.summarySheetsSamples: no visible binding for global variable
‘preferences’
pipeline.summarySheetsSamples: no visible binding for global variable
‘gs.def.list’
pipeline.summarySheetsSamples: no visible binding for global variable
‘gene.info’
pipeline.summarySheetsSamples: no visible global function definition
for ‘hist’
pipeline.summarySheetsSamples: no visible binding for global variable
‘p.g.m’
pipeline.summarySheetsSamples: no visible global function definition
for ‘pdf’
pipeline.summarySheetsSamples: no visible global function definition
for ‘layout’
pipeline.summarySheetsSamples: no visible global function definition
for ‘par’
pipeline.summarySheetsSamples: no visible global function definition
for ‘text’
pipeline.summarySheetsSamples: no visible binding for global variable
‘perc.DE.m’
pipeline.summarySheetsSamples: no visible binding for global variable
‘fdr.g.m’
pipeline.summarySheetsSamples: no visible binding for global variable
‘t.g.m’
pipeline.summarySheetsSamples: no visible global function definition
for ‘image’
pipeline.summarySheetsSamples: no visible binding for global variable
‘metadata’
pipeline.summarySheetsSamples: no visible global function definition
for ‘color.palette.portraits’
pipeline.summarySheetsSamples: no visible global function definition
for ‘axis’
pipeline.summarySheetsSamples: no visible global function definition
for ‘box’
pipeline.summarySheetsSamples: no visible binding for global variable
‘som.result’
pipeline.summarySheetsSamples: no visible global function definition
for ‘rect’
pipeline.summarySheetsSamples: no visible global function definition
for ‘mtext’
pipeline.summarySheetsSamples: no visible global function definition
for ‘abline’
pipeline.summarySheetsSamples: no visible binding for global variable
‘n.0.m’
pipeline.summarySheetsSamples: no visible global function definition
for ‘lines’
pipeline.summarySheetsSamples: no visible binding for global variable
‘Fdr.g.m’
pipeline.summarySheetsSamples: no visible global function definition
for ‘legend’
pipeline.summarySheetsSamples: no visible binding for global variable
‘spot.list.samples’
pipeline.summarySheetsSamples: no visible global function definition
for ‘dev.off’
pipeline.supportingMaps: no visible binding for global variable
‘files.name’
pipeline.supportingMaps: no visible global function definition for
‘pdf’
pipeline.supportingMaps: no visible global function definition for
‘par’
pipeline.supportingMaps: no visible binding for global variable
‘som.result’
pipeline.supportingMaps: no visible global function definition for
‘image’
pipeline.supportingMaps: no visible binding for global variable
‘preferences’
pipeline.supportingMaps: no visible global function definition for
‘color.palette.heatmaps’
pipeline.supportingMaps: no visible global function definition for
‘mtext’
pipeline.supportingMaps: no visible global function definition for
‘box’
pipeline.supportingMaps: no visible global function definition for
‘layout’
pipeline.supportingMaps: no visible global function definition for
‘axis’
pipeline.supportingMaps: no visible binding for global variable
‘metadata’
pipeline.supportingMaps: no visible binding for global variable ‘var’
pipeline.supportingMaps: no visible binding for global variable ‘p.m’
pipeline.supportingMaps: no visible global function definition for
‘colorRampPalette’
pipeline.supportingMaps: no visible global function definition for
‘quantile’
pipeline.supportingMaps : <anonymous>: no visible global function
definition for ‘hist’
pipeline.supportingMaps : <anonymous>: no visible binding for global
variable ‘indata’
pipeline.supportingMaps: no visible global function definition for
‘cor’
pipeline.supportingMaps: no visible binding for global variable
‘indata’
pipeline.supportingMaps : <anonymous>: no visible binding for global
variable ‘metadata’
pipeline.supportingMaps : <anonymous>: no visible binding for global
variable ‘preferences’
pipeline.supportingMaps: no visible global function definition for
‘dev.off’
pipeline.topologyProfiles: no visible binding for global variable
‘metadata’
pipeline.topologyProfiles: no visible binding for global variable
‘files.name’
pipeline.topologyProfiles: no visible binding for global variable
‘group.labels’
pipeline.topologyProfiles: no visible global function definition for
‘pdf’
pipeline.topologyProfiles: no visible global function definition for
‘par’
pipeline.topologyProfiles: no visible binding for global variable
‘preferences’
pipeline.topologyProfiles: no visible global function definition for
‘sd’
pipeline.topologyProfiles: no visible global function definition for
‘barplot’
pipeline.topologyProfiles: no visible binding for global variable
‘group.colors’
pipeline.topologyProfiles: no visible binding for global variable
‘indata’
pipeline.topologyProfiles: no visible global function definition for
‘box’
pipeline.topologyProfiles: no visible global function definition for
‘boxplot’
pipeline.topologyProfiles: no visible binding for global variable
‘groupwise.group.colors’
pipeline.topologyProfiles: no visible global function definition for
‘axis’
pipeline.topologyProfiles : <anonymous>: no visible binding for global
variable ‘group.labels’
pipeline.topologyProfiles : <anonymous>: no visible binding for global
variable ‘preferences’
pipeline.topologyProfiles: no visible global function definition for
‘dev.off’
radarchart: no visible global function definition for ‘polygon’
radarchart: no visible global function definition for ‘text’
radarchart: no visible global function definition for ‘arrows’
radarchart: no visible global function definition for ‘points’
som.linear.init.subdata: no visible global function definition for
‘prcomp’
som.training.phase: no visible global function definition for
‘setTxtProgressBar’
util.cat: no visible global function definition for ‘flush.console’
Undefined global functions or variables:
Fdr.g.m WAD.g.m abline add_edges aov arrows as.dendrogram axis
barplot box boxplot chromosome.list chull col2rgb
color.palette.heatmaps color.palette.portraits colorRampPalette combn
cor csv.function cutree data density dev.off dist ecdf env fdr.g.m
files.name fisher.test flush.console frame gene.info get.edgelist
graph.empty group.colors group.labels group.silhouette.coef
groupwise.group.colors gs.def.list hclust head hist image indata
indata.gene.mean indata.sample.mean is kmeans layout legend lines
metadata modifyList mtext n.0.m na.omit opossom.genesets
order.dendrogram output.paths p.g.m p.m par pat.labels pbeta pdf
perc.DE.m persp pie points polygon prcomp preferences pt quantile
rect reorder rgb samples.GSZ.scores sd sessionInfo setTxtProgressBar
som.result spot.list.correlation spot.list.dmap
spot.list.group.overexpression spot.list.kmeans
spot.list.overexpression spot.list.samples spot.list.underexpression
t.ensID.m t.g.m t.m text title unique.protein.ids v var wilcox.test
write.csv write.csv2
Consider adding
importFrom("grDevices", "chull", "col2rgb", "colorRampPalette",
"dev.off", "pdf", "rgb")
importFrom("graphics", "abline", "arrows", "axis", "barplot", "box",
"boxplot", "frame", "hist", "image", "layout", "legend",
"lines", "mtext", "par", "persp", "pie", "points",
"polygon", "rect", "text", "title")
importFrom("methods", "is")
importFrom("stats", "aov", "as.dendrogram", "cor", "cutree", "density",
"dist", "ecdf", "fisher.test", "hclust", "kmeans",
"na.omit", "order.dendrogram", "pbeta", "prcomp", "pt",
"quantile", "reorder", "sd", "var", "wilcox.test")
importFrom("utils", "combn", "data", "flush.console", "head",
"modifyList", "sessionInfo", "setTxtProgressBar",
"write.csv", "write.csv2")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘GeneSet.Fisher’ ‘GeneSet.GSZ’ ‘GeneSet.maxmean’
‘Get.Running.Average’ ‘Quantile.Normalization’ ‘Smooth.Matrix’
‘_oposSOM_calculateDelta’ ‘_oposSOM_calculateEuclideanDistances’
‘_oposSOM_calculateNeighborhoodMatrix’
‘_oposSOM_matrixToCodebookMatrix’ ‘biomart.available’
‘calculateDelta’ ‘calculateEuclideanDistances’
‘calculateNeighborhoodMatrix’ ‘col.pix’ ‘get.beta.statistic’
‘get.neighbors’ ‘heatmap’ ‘heatmap.A4’ ‘matrixToCodebookMatrix’
‘modules.CSV.sheets’ ‘modules.chromosomes’ ‘modules.profiles’
‘modules.relations’ ‘modules.report.sheets’ ‘newProgressBar’
‘pipeline.affymetrixQualityCheck’ ‘pipeline.calcStatistics’
‘pipeline.cancerHallmarks’ ‘pipeline.checkInputParameters’
‘pipeline.chromosomeExpressionReports’
‘pipeline.detectEnsemblDataset’ ‘pipeline.detectSpotsIntegral’
‘pipeline.detectSpotsSamples’ ‘pipeline.differenceAnalyses’
‘pipeline.entropyProfiles’ ‘pipeline.geneLists’
‘pipeline.generateSOM’ ‘pipeline.genesetOverviews’
‘pipeline.genesetProfilesAndMaps’ ‘pipeline.genesetStatisticIntegral’
‘pipeline.genesetStatisticSamples’ ‘pipeline.groupAnalysis’
‘pipeline.groupAssignment’ ‘pipeline.groupSpecificGenesets’
‘pipeline.htmlDifferencesSummary’ ‘pipeline.htmlGenesetAnalysis’
‘pipeline.htmlGroupSummary’ ‘pipeline.htmlModuleSummary’
‘pipeline.htmlSampleSummary’ ‘pipeline.htmlSummary’
‘pipeline.moduleCorrelationMap’ ‘pipeline.patAssignment’
‘pipeline.prepareAnnotation’ ‘pipeline.prepareIndata’
‘pipeline.qualityCheck’ ‘pipeline.sampleExpressionPortraits’
‘pipeline.sampleSimilarityAnalysisCor’
‘pipeline.sampleSimilarityAnalysisED’
‘pipeline.sampleSimilarityAnalysisICA’
‘pipeline.sampleSimilarityAnalysisSOM’ ‘pipeline.summarySheetsGroups’
‘pipeline.summarySheetsModules’ ‘pipeline.summarySheetsPATs’
‘pipeline.summarySheetsSamples’ ‘pipeline.supportingMaps’
‘pipeline.topologyProfiles’ ‘radarchart’ ‘som.linear.init’
‘som.linear.init.subdata’ ‘som.training’ ‘som.training.phase’
‘sort.label’ ‘util.call’ ‘util.cat’ ‘util.fatal’ ‘util.info’
‘util.load’ ‘util.log’ ‘util.progress’ ‘util.progress.terminate’
‘util.save’ ‘util.warn’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... WARNING
Found the following file(s) containing GNU extensions:
src/Makevars
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif, .NOTPARALLEL See section ‘Writing portable
packages’ in the ‘Writing R Extensions’ manual.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
oposSOM-package 138.749 376.346 97.528
opossom.run 30.854 25.722 38.026
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 WARNINGs, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.12-bioc/meat/oposSOM.Rcheck/00check.log’
for details.
