CHECK report for oposSOM on malbec1
This page was generated on 2018-04-12 13:12:22 -0400 (Thu, 12 Apr 2018).
oposSOM 1.16.0
Henry Loeffler-Wirth
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/oposSOM |
| Branch: RELEASE_3_6 |
| Last Commit: 17b5341 |
| Last Changed Date: 2017-10-30 12:40:18 -0400 (Mon, 30 Oct 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | |
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
Summary
Command output
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###
### Running command:
###
### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings oposSOM_1.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/oposSOM.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘oposSOM/DESCRIPTION’ ... OK
* this is package ‘oposSOM’ version ‘1.16.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘oposSOM’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GeneSet.Fisher : fn: no visible global function definition for
‘fisher.test’
Smooth.Matrix: no visible binding for global variable ‘v’
biomart.available: no visible binding for global variable ‘preferences’
get.beta.statistic: no visible global function definition for ‘pbeta’
heatmap: no visible binding for global variable ‘dist’
heatmap: no visible binding for global variable ‘hclust’
heatmap : <anonymous>: no visible global function definition for
‘reorder’
heatmap: no visible global function definition for ‘as.dendrogram’
heatmap: no visible global function definition for ‘order.dendrogram’
heatmap: no visible binding for global variable ‘sd’
heatmap: no visible global function definition for ‘par’
heatmap: no visible global function definition for ‘layout’
heatmap: no visible global function definition for ‘image’
heatmap: no visible global function definition for ‘axis’
heatmap: no visible global function definition for ‘mtext’
heatmap: no visible global function definition for ‘plot’
heatmap: no visible global function definition for ‘frame’
heatmap: no visible global function definition for ‘title’
modules.CSV.sheets : <anonymous>: no visible binding for global
variable ‘indata’
modules.CSV.sheets : <anonymous>: no visible global function definition
for ‘cor’
modules.CSV.sheets: no visible binding for global variable ‘indata’
modules.CSV.sheets: no visible global function definition for ‘pt’
modules.CSV.sheets: no visible binding for global variable ‘gene.info’
modules.CSV.sheets: no visible binding for global variable
‘indata.gene.mean’
modules.CSV.sheets: no visible binding for global variable ‘sd’
modules.CSV.sheets: no visible global function definition for
‘write.csv2’
modules.chromosomes: no visible binding for global variable
‘chromosome.list’
modules.chromosomes: no visible global function definition for ‘pdf’
modules.chromosomes : <anonymous>: no visible binding for global
variable ‘chromosome.list’
modules.chromosomes: no visible global function definition for
‘colorRampPalette’
modules.chromosomes: no visible binding for global variable ‘head’
modules.chromosomes: no visible global function definition for ‘par’
modules.chromosomes: no visible global function definition for ‘image’
modules.chromosomes: no visible global function definition for ‘title’
modules.chromosomes: no visible global function definition for ‘box’
modules.chromosomes: no visible global function definition for ‘abline’
modules.chromosomes: no visible global function definition for ‘axis’
modules.chromosomes: no visible global function definition for ‘layout’
modules.chromosomes: no visible global function definition for ‘plot’
modules.chromosomes: no visible global function definition for ‘text’
modules.chromosomes: no visible global function definition for
‘dev.off’
modules.profiles: no visible global function definition for ‘sd’
modules.profiles: no visible global function definition for ‘pdf’
modules.profiles: no visible global function definition for ‘layout’
modules.profiles: no visible global function definition for ‘par’
modules.profiles: no visible global function definition for ‘image’
modules.profiles: no visible binding for global variable ‘preferences’
modules.profiles: no visible global function definition for ‘axis’
modules.profiles: no visible global function definition for ‘box’
modules.profiles: no visible global function definition for ‘barplot’
modules.profiles: no visible binding for global variable ‘group.colors’
modules.profiles: no visible binding for global variable ‘indata’
modules.profiles: no visible global function definition for ‘abline’
modules.profiles: no visible binding for global variable ‘group.labels’
modules.profiles: no visible global function definition for ‘text’
modules.profiles: no visible binding for global variable
‘groupwise.group.colors’
modules.profiles: no visible global function definition for ‘plot’
modules.profiles: no visible global function definition for ‘boxplot’
modules.profiles: no visible global function definition for ‘dev.off’
modules.relations: no visible global function definition for ‘sd’
modules.relations: no visible global function definition for ‘pdf’
modules.relations: no visible global function definition for ‘cor’
modules.relations: no visible global function definition for ‘layout’
modules.relations: no visible global function definition for ‘par’
modules.relations: no visible global function definition for ‘image’
modules.relations: no visible binding for global variable ‘preferences’
modules.relations: no visible global function definition for ‘box’
modules.relations: no visible global function definition for ‘plot’
modules.relations: no visible global function definition for ‘legend’
modules.relations: no visible global function definition for ‘as’
modules.relations: no visible binding for global variable
‘group.labels’
modules.relations: no visible global function definition for
‘graph.empty’
modules.relations: no visible global function definition for
‘add_edges’
modules.relations: no visible binding for global variable
‘groupwise.group.colors’
modules.relations: no visible global function definition for ‘title’
modules.relations: no visible global function definition for ‘frame’
modules.relations: no visible global function definition for ‘text’
modules.relations: no visible global function definition for ‘barplot’
modules.relations: no visible global function definition for ‘dev.off’
modules.report.sheets: no visible global function definition for ‘pdf’
modules.report.sheets: no visible global function definition for
‘layout’
modules.report.sheets: no visible global function definition for ‘par’
modules.report.sheets: no visible global function definition for
‘color.palette.portraits’
modules.report.sheets: no visible global function definition for
‘colorRampPalette’
modules.report.sheets: no visible global function definition for
‘image’
modules.report.sheets: no visible binding for global variable
‘preferences’
modules.report.sheets: no visible global function definition for
‘mtext’
modules.report.sheets: no visible global function definition for ‘box’
modules.report.sheets: no visible global function definition for ‘plot’
modules.report.sheets: no visible global function definition for
‘points’
modules.report.sheets: no visible global function definition for ‘text’
modules.report.sheets : <anonymous>: no visible global function
definition for ‘head’
modules.report.sheets: no visible global function definition for
‘legend’
modules.report.sheets: no visible binding for global variable ‘indata’
modules.report.sheets: no visible global function definition for
‘color.palette.heatmaps’
modules.report.sheets: no visible global function definition for ‘axis’
modules.report.sheets: no visible binding for global variable
‘group.labels’
modules.report.sheets: no visible binding for global variable
‘group.colors’
modules.report.sheets: no visible global function definition for
‘frame’
modules.report.sheets: no visible global function definition for ‘sd’
modules.report.sheets: no visible global function definition for ‘cor’
modules.report.sheets: no visible binding for global variable
‘metadata’
modules.report.sheets: no visible global function definition for
‘barplot’
modules.report.sheets : <anonymous>: no visible binding for global
variable ‘indata’
modules.report.sheets : <anonymous>: no visible global function
definition for ‘cor’
modules.report.sheets: no visible global function definition for ‘rect’
modules.report.sheets: no visible binding for global variable
‘gene.info’
modules.report.sheets: no visible binding for global variable
‘gs.def.list’
modules.report.sheets : <anonymous>: no visible binding for global
variable ‘gene.info’
modules.report.sheets: no visible global function definition for ‘hist’
modules.report.sheets: no visible global function definition for
‘abline’
modules.report.sheets: no visible global function definition for
‘lines’
modules.report.sheets: no visible global function definition for
‘dev.off’
opossom.new: no visible global function definition for ‘modifyList’
opossom.run: no visible global function definition for ‘sessionInfo’
pipeline.affymetrixQualityCheck: no visible binding for global variable
‘indata’
pipeline.affymetrixQualityCheck: no visible global function definition
for ‘par’
pipeline.affymetrixQualityCheck: no visible global function definition
for ‘barplot’
pipeline.affymetrixQualityCheck: no visible binding for global variable
‘group.colors’
pipeline.affymetrixQualityCheck: no visible global function definition
for ‘box’
pipeline.affymetrixQualityCheck: no visible binding for global variable
‘group.labels’
pipeline.affymetrixQualityCheck: no visible global function definition
for ‘boxplot’
pipeline.affymetrixQualityCheck: no visible binding for global variable
‘groupwise.group.colors’
pipeline.affymetrixQualityCheck: no visible global function definition
for ‘axis’
pipeline.affymetrixQualityCheck: no visible global function definition
for ‘abline’
pipeline.affymetrixQualityCheck: no visible global function definition
for ‘plot’
pipeline.affymetrixQualityCheck: no visible global function definition
for ‘lines’
pipeline.calcStatistics: no visible binding for '<<-' assignment to
‘WAD.g.m’
pipeline.calcStatistics: no visible binding for global variable
‘indata’
pipeline.calcStatistics: no visible binding for global variable
‘WAD.g.m’
pipeline.calcStatistics: no visible binding for '<<-' assignment to
‘t.g.m’
pipeline.calcStatistics: no visible binding for '<<-' assignment to
‘p.g.m’
pipeline.calcStatistics: no visible binding for '<<-' assignment to
‘n.0.m’
pipeline.calcStatistics: no visible binding for global variable ‘n.0.m’
pipeline.calcStatistics: no visible binding for '<<-' assignment to
‘perc.DE.m’
pipeline.calcStatistics: no visible binding for global variable
‘perc.DE.m’
pipeline.calcStatistics: no visible binding for '<<-' assignment to
‘fdr.g.m’
pipeline.calcStatistics: no visible binding for '<<-' assignment to
‘Fdr.g.m’
pipeline.calcStatistics: no visible binding for global variable
‘indata.gene.mean’
pipeline.calcStatistics: no visible binding for global variable ‘sd’
pipeline.calcStatistics: no visible binding for global variable ‘t.g.m’
pipeline.calcStatistics: no visible binding for global variable ‘p.g.m’
pipeline.calcStatistics: no visible binding for global variable
‘fdr.g.m’
pipeline.calcStatistics: no visible binding for global variable
‘Fdr.g.m’
pipeline.calcStatistics: no visible binding for '<<-' assignment to
‘t.m’
pipeline.calcStatistics: no visible binding for '<<-' assignment to
‘p.m’
pipeline.calcStatistics: no visible binding for global variable
‘preferences’
pipeline.calcStatistics: no visible binding for global variable
‘som.result’
pipeline.calcStatistics: no visible binding for global variable ‘t.m’
pipeline.calcStatistics: no visible global function definition for
‘na.omit’
pipeline.calcStatistics: no visible binding for global variable ‘p.m’
pipeline.cancerHallmarks : <anonymous>: no visible binding for global
variable ‘gs.def.list’
pipeline.cancerHallmarks : <anonymous>: no visible binding for global
variable ‘gene.info’
pipeline.cancerHallmarks: no visible binding for global variable
‘indata’
pipeline.cancerHallmarks : <anonymous>: no visible binding for global
variable ‘unique.protein.ids’
pipeline.cancerHallmarks : <anonymous>: no visible binding for global
variable ‘t.ensID.m’
pipeline.cancerHallmarks: no visible binding for global variable
‘preferences’
pipeline.cancerHallmarks : <anonymous>: no visible global function
definition for ‘na.omit’
pipeline.cancerHallmarks: no visible binding for global variable
‘files.name’
pipeline.cancerHallmarks: no visible global function definition for
‘pdf’
pipeline.cancerHallmarks: no visible global function definition for
‘layout’
pipeline.cancerHallmarks: no visible binding for global variable
‘group.labels’
pipeline.cancerHallmarks: no visible global function definition for
‘par’
pipeline.cancerHallmarks: no visible global function definition for
‘boxplot’
pipeline.cancerHallmarks: no visible binding for global variable
‘groupwise.group.colors’
pipeline.cancerHallmarks: no visible global function definition for
‘abline’
pipeline.cancerHallmarks: no visible binding for global variable
‘som.result’
pipeline.cancerHallmarks: no visible global function definition for
‘color.palette.heatmaps’
pipeline.cancerHallmarks: no visible global function definition for
‘na.omit’
pipeline.cancerHallmarks: no visible global function definition for
‘plot’
pipeline.cancerHallmarks: no visible global function definition for
‘title’
pipeline.cancerHallmarks: no visible global function definition for
‘box’
pipeline.cancerHallmarks: no visible global function definition for
‘frame’
pipeline.cancerHallmarks: no visible global function definition for
‘legend’
pipeline.cancerHallmarks: no visible global function definition for
‘dev.off’
pipeline.checkInputParameters: no visible binding for global variable
‘env’
pipeline.checkInputParameters : <anonymous>: no visible binding for
global variable ‘indata’
pipeline.checkInputParameters : <anonymous> : <anonymous>: no visible
global function definition for ‘na.omit’
pipeline.checkInputParameters: no visible binding for global variable
‘indata’
pipeline.checkInputParameters: no visible binding for '<<-' assignment
to ‘group.labels’
pipeline.checkInputParameters: no visible binding for '<<-' assignment
to ‘group.colors’
pipeline.checkInputParameters: no visible binding for '<<-' assignment
to ‘indata’
pipeline.checkInputParameters: no visible binding for global variable
‘group.labels’
pipeline.checkInputParameters: no visible binding for global variable
‘group.colors’
pipeline.checkInputParameters: no visible global function definition
for ‘colorRampPalette’
pipeline.checkInputParameters: no visible global function definition
for ‘col2rgb’
pipeline.checkInputParameters : <anonymous>: no visible global function
definition for ‘rgb’
pipeline.checkInputParameters: no visible binding for '<<-' assignment
to ‘groupwise.group.colors’
pipeline.checkInputParameters: no visible binding for global variable
‘groupwise.group.colors’
pipeline.checkInputParameters: no visible binding for global variable
‘color.palette.portraits’
pipeline.checkInputParameters: no visible binding for '<<-' assignment
to ‘color.palette.portraits’
pipeline.checkInputParameters: no visible binding for global variable
‘color.palette.heatmaps’
pipeline.checkInputParameters: no visible binding for '<<-' assignment
to ‘color.palette.heatmaps’
pipeline.checkInputParameters: no visible binding for '<<-' assignment
to ‘files.name’
pipeline.checkInputParameters: no visible binding for global variable
‘files.name’
pipeline.checkInputParameters: no visible binding for '<<-' assignment
to ‘output.paths’
pipeline.chromosomeExpressionReports: no visible binding for global
variable ‘chromosome.list’
pipeline.chromosomeExpressionReports : <anonymous>: no visible binding
for global variable ‘gene.info’
pipeline.chromosomeExpressionReports: no visible binding for global
variable ‘indata’
pipeline.chromosomeExpressionReports : <anonymous>: no visible binding
for global variable ‘indata’
pipeline.chromosomeExpressionReports: no visible global function
definition for ‘hclust’
pipeline.chromosomeExpressionReports: no visible global function
definition for ‘dist’
pipeline.chromosomeExpressionReports: no visible binding for global
variable ‘files.name’
pipeline.chromosomeExpressionReports: no visible global function
definition for ‘pdf’
pipeline.chromosomeExpressionReports: no visible global function
definition for ‘layout’
pipeline.chromosomeExpressionReports: no visible global function
definition for ‘par’
pipeline.chromosomeExpressionReports: no visible global function
definition for ‘image’
pipeline.chromosomeExpressionReports: no visible global function
definition for ‘color.palette.heatmaps’
pipeline.chromosomeExpressionReports: no visible global function
definition for ‘box’
pipeline.chromosomeExpressionReports: no visible global function
definition for ‘abline’
pipeline.chromosomeExpressionReports: no visible global function
definition for ‘axis’
pipeline.chromosomeExpressionReports: no visible binding for global
variable ‘group.colors’
pipeline.chromosomeExpressionReports: no visible global function
definition for ‘dev.off’
pipeline.detectEnsemblDataset: no visible binding for '<<-' assignment
to ‘preferences’
pipeline.detectEnsemblDataset: no visible binding for global variable
‘preferences’
pipeline.detectEnsemblDataset: no visible binding for global variable
‘indata’
pipeline.detectSpotsIntegral: no visible binding for global variable
‘metadata’
pipeline.detectSpotsIntegral: no visible binding for global variable
‘indata’
pipeline.detectSpotsIntegral: no visible binding for global variable
‘preferences’
pipeline.detectSpotsIntegral: no visible binding for '<<-' assignment
to ‘spot.list.overexpression’
pipeline.detectSpotsIntegral: no visible binding for global variable
‘spot.list.overexpression’
pipeline.detectSpotsIntegral: no visible binding for global variable
‘som.result’
pipeline.detectSpotsIntegral : <anonymous>: no visible binding for
global variable ‘metadata’
pipeline.detectSpotsIntegral : <anonymous>: no visible binding for
global variable ‘indata’
pipeline.detectSpotsIntegral: no visible binding for '<<-' assignment
to ‘spot.list.underexpression’
pipeline.detectSpotsIntegral: no visible binding for global variable
‘spot.list.underexpression’
pipeline.detectSpotsIntegral: no visible binding for '<<-' assignment
to ‘spot.list.correlation’
pipeline.detectSpotsIntegral: no visible binding for global variable
‘spot.list.correlation’
pipeline.detectSpotsIntegral: no visible global function definition for
‘cor’
pipeline.detectSpotsIntegral: no visible global function definition for
‘kmeans’
pipeline.detectSpotsIntegral: no visible binding for '<<-' assignment
to ‘spot.list.kmeans’
pipeline.detectSpotsIntegral: no visible binding for global variable
‘spot.list.kmeans’
pipeline.detectSpotsIntegral: no visible binding for global variable
‘group.labels’
pipeline.detectSpotsIntegral: no visible binding for '<<-' assignment
to ‘spot.list.group.overexpression’
pipeline.detectSpotsIntegral: no visible binding for global variable
‘spot.list.group.overexpression’
pipeline.detectSpotsIntegral : <anonymous>: no visible binding for
global variable ‘preferences’
pipeline.detectSpotsIntegral : <anonymous>: no visible global function
definition for ‘dist’
pipeline.detectSpotsIntegral: no visible binding for '<<-' assignment
to ‘spot.list.dmap’
pipeline.detectSpotsIntegral: no visible binding for global variable
‘spot.list.dmap’
pipeline.detectSpotsIntegral: no visible global function definition for
‘na.omit’
pipeline.detectSpotsIntegral : <anonymous>: no visible global function
definition for ‘sd’
pipeline.detectSpotsIntegral : <anonymous>: no visible binding for
global variable ‘spot.list.dmap’
pipeline.detectSpotsSamples: no visible binding for '<<-' assignment to
‘spot.list.samples’
pipeline.detectSpotsSamples: no visible binding for global variable
‘indata’
pipeline.detectSpotsSamples: no visible binding for global variable
‘spot.list.samples’
pipeline.differenceAnalyses: no visible global function definition for
‘combn’
pipeline.differenceAnalyses: no visible binding for global variable
‘files.name’
pipeline.differenceAnalyses: no visible binding for global variable
‘var’
pipeline.differenceAnalyses: no visible global function definition for
‘pt’
pipeline.entropyProfiles: no visible binding for global variable
‘files.name’
pipeline.entropyProfiles: no visible global function definition for
‘pdf’
pipeline.entropyProfiles: no visible global function definition for
‘par’
pipeline.entropyProfiles: no visible global function definition for
‘barplot’
pipeline.entropyProfiles: no visible binding for global variable
‘metadata’
pipeline.entropyProfiles: no visible binding for global variable
‘group.colors’
pipeline.entropyProfiles: no visible binding for global variable
‘indata’
pipeline.entropyProfiles: no visible global function definition for
‘box’
pipeline.entropyProfiles: no visible binding for global variable
‘group.labels’
pipeline.entropyProfiles: no visible global function definition for
‘boxplot’
pipeline.entropyProfiles: no visible binding for global variable
‘groupwise.group.colors’
pipeline.entropyProfiles: no visible global function definition for
‘axis’
pipeline.entropyProfiles: no visible binding for global variable ‘var’
pipeline.entropyProfiles: no visible global function definition for
‘quantile’
pipeline.entropyProfiles : <anonymous>: no visible global function
definition for ‘hist’
pipeline.entropyProfiles : <anonymous>: no visible binding for global
variable ‘preferences’
pipeline.entropyProfiles: no visible binding for global variable
‘som.result’
pipeline.entropyProfiles: no visible global function definition for
‘dev.off’
pipeline.geneLists: no visible binding for global variable ‘som.result’
pipeline.geneLists: no visible binding for global variable ‘indata’
pipeline.geneLists: no visible binding for global variable ‘gene.info’
pipeline.geneLists: no visible binding for global variable
‘indata.gene.mean’
pipeline.geneLists: no visible binding for global variable ‘files.name’
pipeline.geneLists: no visible global function definition for
‘write.csv2’
pipeline.geneLists: no visible binding for global variable
‘output.paths’
pipeline.geneLists: no visible binding for global variable
‘samples.GSZ.scores’
pipeline.geneLists: no visible binding for global variable
‘preferences’
pipeline.geneLists: no visible binding for global variable ‘p.g.m’
pipeline.geneLists: no visible binding for global variable ‘WAD.g.m’
pipeline.geneLists: no visible binding for global variable ‘t.g.m’
pipeline.geneLists: no visible binding for global variable ‘fdr.g.m’
pipeline.geneLists: no visible binding for global variable ‘Fdr.g.m’
pipeline.geneLists: no visible binding for global variable ‘perc.DE.m’
pipeline.geneLists: no visible binding for global variable
‘spot.list.samples’
pipeline.generateSOM: no visible binding for '<<-' assignment to
‘som.result’
pipeline.generateSOM: no visible binding for global variable ‘indata’
pipeline.generateSOM: no visible binding for global variable
‘preferences’
pipeline.generateSOM: no visible binding for global variable
‘som.result’
pipeline.generateSOM: no visible binding for '<<-' assignment to
‘metadata’
pipeline.generateSOM: no visible binding for global variable ‘metadata’
pipeline.generateSOM: no visible binding for '<<-' assignment to
‘gene.info’
pipeline.generateSOM: no visible binding for global variable
‘gene.info’
pipeline.genesetOverviews: no visible binding for global variable
‘files.name’
pipeline.genesetOverviews: no visible global function definition for
‘pdf’
pipeline.genesetOverviews: no visible binding for global variable
‘preferences’
pipeline.genesetOverviews : <anonymous>: no visible binding for global
variable ‘gs.def.list’
pipeline.genesetOverviews: no visible binding for global variable
‘gs.def.list’
pipeline.genesetOverviews: no visible binding for global variable
‘samples.GSZ.scores’
pipeline.genesetOverviews: no visible binding for global variable
‘indata’
pipeline.genesetOverviews: no visible global function definition for
‘quantile’
pipeline.genesetOverviews: no visible global function definition for
‘color.palette.heatmaps’
pipeline.genesetOverviews: no visible binding for global variable
‘group.colors’
pipeline.genesetOverviews: no visible global function definition for
‘par’
pipeline.genesetOverviews: no visible global function definition for
‘image’
pipeline.genesetOverviews: no visible global function definition for
‘box’
pipeline.genesetOverviews: no visible global function definition for
‘axis’
pipeline.genesetOverviews: no visible global function definition for
‘mtext’
pipeline.genesetOverviews: no visible binding for global variable
‘group.labels’
pipeline.genesetOverviews : <anonymous>: no visible binding for global
variable ‘group.labels’
pipeline.genesetOverviews : <anonymous>: no visible global function
definition for ‘hclust’
pipeline.genesetOverviews : <anonymous>: no visible global function
definition for ‘dist’
pipeline.genesetOverviews: no visible binding for global variable
‘spot.list.samples’
pipeline.genesetOverviews: no visible global function definition for
‘hist’
pipeline.genesetOverviews: no visible global function definition for
‘abline’
pipeline.genesetOverviews: no visible global function definition for
‘plot’
pipeline.genesetOverviews: no visible global function definition for
‘lines’
pipeline.genesetOverviews: no visible global function definition for
‘legend’
pipeline.genesetOverviews: no visible global function definition for
‘dev.off’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
‘samples.GSZ.scores’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
‘files.name’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘quantile’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘sd’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
‘gs.def.list’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘pdf’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘layout’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
‘indata’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
‘gene.info’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
‘sd’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘hclust’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘dist’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘par’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘barplot’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
‘group.colors’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘abline’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘axis’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘mtext’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘frame’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘legend’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
‘groupwise.group.colors’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘image’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘box’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘color.palette.heatmaps’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
‘preferences’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
‘som.result’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘na.omit’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘plot’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘title’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
‘group.labels’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘boxplot’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘dev.off’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘write.csv2’
pipeline.genesetStatisticIntegral : spot.fisher.p: no visible global
function definition for ‘na.omit’
pipeline.genesetStatisticIntegral : spot.fisher.p: no visible binding
for global variable ‘gene.info’
pipeline.genesetStatisticIntegral : spot.fisher.p: no visible binding
for global variable ‘unique.protein.ids’
pipeline.genesetStatisticIntegral : spot.fisher.p: no visible binding
for global variable ‘gs.def.list’
pipeline.genesetStatisticIntegral: no visible binding for '<<-'
assignment to ‘spot.list.overexpression’
pipeline.genesetStatisticIntegral: no visible binding for global
variable ‘spot.list.overexpression’
pipeline.genesetStatisticIntegral: no visible binding for '<<-'
assignment to ‘spot.list.underexpression’
pipeline.genesetStatisticIntegral: no visible binding for global
variable ‘spot.list.underexpression’
pipeline.genesetStatisticIntegral: no visible binding for global
variable ‘spot.list.correlation’
pipeline.genesetStatisticIntegral: no visible binding for '<<-'
assignment to ‘spot.list.correlation’
pipeline.genesetStatisticIntegral: no visible binding for '<<-'
assignment to ‘spot.list.kmeans’
pipeline.genesetStatisticIntegral: no visible binding for global
variable ‘spot.list.kmeans’
pipeline.genesetStatisticIntegral: no visible binding for global
variable ‘group.labels’
pipeline.genesetStatisticIntegral: no visible binding for '<<-'
assignment to ‘spot.list.group.overexpression’
pipeline.genesetStatisticIntegral: no visible binding for global
variable ‘spot.list.group.overexpression’
pipeline.genesetStatisticIntegral: no visible binding for '<<-'
assignment to ‘spot.list.dmap’
pipeline.genesetStatisticIntegral: no visible binding for global
variable ‘spot.list.dmap’
pipeline.genesetStatisticSamples: no visible binding for '<<-'
assignment to ‘t.ensID.m’
pipeline.genesetStatisticSamples: no visible binding for global
variable ‘t.g.m’
pipeline.genesetStatisticSamples: no visible binding for global
variable ‘indata’
pipeline.genesetStatisticSamples: no visible binding for global
variable ‘gene.info’
pipeline.genesetStatisticSamples: no visible binding for global
variable ‘t.ensID.m’
pipeline.genesetStatisticSamples: no visible binding for global
variable ‘preferences’
pipeline.genesetStatisticSamples: no visible binding for global
variable ‘gs.def.list’
pipeline.genesetStatisticSamples: no visible binding for global
variable ‘unique.protein.ids’
pipeline.genesetStatisticSamples : <anonymous>: no visible binding for
global variable ‘t.ensID.m’
pipeline.genesetStatisticSamples : <anonymous>: no visible binding for
global variable ‘unique.protein.ids’
pipeline.genesetStatisticSamples: no visible global function definition
for ‘ecdf’
pipeline.genesetStatisticSamples: no visible binding for '<<-'
assignment to ‘spot.list.samples’
pipeline.genesetStatisticSamples: no visible binding for global
variable ‘spot.list.samples’
pipeline.genesetStatisticSamples : <anonymous>: no visible binding for
global variable ‘spot.list.samples’
pipeline.genesetStatisticSamples : <anonymous>: no visible binding for
global variable ‘gs.def.list’
pipeline.genesetStatisticSamples : <anonymous>: no visible binding for
global variable ‘preferences’
pipeline.genesetStatisticSamples: no visible binding for '<<-'
assignment to ‘samples.GSZ.scores’
pipeline.groupAnalysis: no visible binding for global variable
‘files.name’
pipeline.groupAnalysis : <anonymous>: no visible global function
definition for ‘sd’
pipeline.groupAnalysis: no visible global function definition for ‘pt’
pipeline.groupAssignment: no visible binding for global variable
‘group.labels’
pipeline.groupAssignment: no visible binding for global variable
‘pat.labels’
pipeline.groupAssignment: no visible binding for global variable
‘preferences’
pipeline.groupAssignment: no visible binding for global variable
‘indata’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
‘group.labels’
pipeline.groupAssignment: no visible binding for global variable
‘files.name’
pipeline.groupAssignment: no visible global function definition for
‘pdf’
pipeline.groupAssignment: no visible global function definition for
‘barplot’
pipeline.groupAssignment: no visible global function definition for
‘box’
pipeline.groupAssignment: no visible global function definition for
‘lines’
pipeline.groupAssignment: no visible global function definition for
‘abline’
pipeline.groupAssignment: no visible global function definition for
‘dev.off’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
‘pat.labels’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
‘group.colors’
pipeline.groupAssignment: no visible binding for global variable
‘group.colors’
pipeline.groupAssignment: no visible global function definition for
‘colorRampPalette’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
‘groupwise.group.colors’
pipeline.groupAssignment: no visible binding for global variable
‘groupwise.group.colors’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
‘t.g.m’
pipeline.groupAssignment: no visible binding for global variable
‘t.g.m’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
‘p.g.m’
pipeline.groupAssignment: no visible binding for global variable
‘p.g.m’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
‘fdr.g.m’
pipeline.groupAssignment: no visible binding for global variable
‘fdr.g.m’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
‘Fdr.g.m’
pipeline.groupAssignment: no visible binding for global variable
‘Fdr.g.m’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
‘WAD.g.m’
pipeline.groupAssignment: no visible binding for global variable
‘WAD.g.m’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
‘n.0.m’
pipeline.groupAssignment: no visible binding for global variable
‘n.0.m’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
‘perc.DE.m’
pipeline.groupAssignment: no visible binding for global variable
‘perc.DE.m’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
‘t.m’
pipeline.groupAssignment: no visible binding for global variable ‘t.m’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
‘p.m’
pipeline.groupAssignment: no visible binding for global variable ‘p.m’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
‘indata’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
‘metadata’
pipeline.groupAssignment: no visible binding for global variable
‘metadata’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
‘indata.sample.mean’
pipeline.groupAssignment: no visible binding for global variable
‘indata.sample.mean’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
‘spot.list.samples’
pipeline.groupAssignment: no visible binding for global variable
‘spot.list.samples’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
‘group.silhouette.coef’
pipeline.groupAssignment: no visible global function definition for
‘cor’
pipeline.groupAssignment : <anonymous>: no visible binding for global
variable ‘group.labels’
pipeline.groupAssignment: no visible binding for global variable
‘group.silhouette.coef’
pipeline.groupSpecificGenesets: no visible global function definition
for ‘sd’
pipeline.groupSpecificGenesets: no visible binding for global variable
‘samples.GSZ.scores’
pipeline.groupSpecificGenesets: no visible binding for global variable
‘group.labels’
pipeline.groupSpecificGenesets : <anonymous>: no visible global
function definition for ‘wilcox.test’
pipeline.groupSpecificGenesets : <anonymous>: no visible binding for
global variable ‘group.labels’
pipeline.groupSpecificGenesets: no visible global function definition
for ‘pdf’
pipeline.groupSpecificGenesets: no visible binding for global variable
‘files.name’
pipeline.groupSpecificGenesets: no visible global function definition
for ‘layout’
pipeline.groupSpecificGenesets: no visible global function definition
for ‘par’
pipeline.groupSpecificGenesets: no visible global function definition
for ‘barplot’
pipeline.groupSpecificGenesets: no visible binding for global variable
‘group.colors’
pipeline.groupSpecificGenesets: no visible binding for global variable
‘indata’
pipeline.groupSpecificGenesets: no visible global function definition
for ‘abline’
pipeline.groupSpecificGenesets: no visible global function definition
for ‘title’
pipeline.groupSpecificGenesets: no visible global function definition
for ‘mtext’
pipeline.groupSpecificGenesets: no visible binding for global variable
‘preferences’
pipeline.groupSpecificGenesets: no visible binding for global variable
‘som.result’
pipeline.groupSpecificGenesets: no visible binding for global variable
‘gene.info’
pipeline.groupSpecificGenesets: no visible binding for global variable
‘gs.def.list’
pipeline.groupSpecificGenesets: no visible global function definition
for ‘plot’
pipeline.groupSpecificGenesets: no visible global function definition
for ‘na.omit’
pipeline.groupSpecificGenesets: no visible global function definition
for ‘color.palette.heatmaps’
pipeline.groupSpecificGenesets: no visible global function definition
for ‘box’
pipeline.groupSpecificGenesets: no visible global function definition
for ‘dev.off’
pipeline.groupSpecificGenesets: no visible global function definition
for ‘write.csv2’
pipeline.groupSpecificGenesets : <anonymous>: no visible global
function definition for ‘aov’
pipeline.groupSpecificGenesets: no visible global function definition
for ‘text’
pipeline.groupSpecificGenesets: no visible binding for global variable
‘groupwise.group.colors’
pipeline.htmlDifferencesSummary: no visible binding for global variable
‘files.name’
pipeline.htmlDifferencesSummary: no visible binding for global variable
‘indata’
pipeline.htmlGenesetAnalysis: no visible binding for global variable
‘preferences’
pipeline.htmlGenesetAnalysis: no visible binding for global variable
‘files.name’
pipeline.htmlGenesetAnalysis: no visible binding for global variable
‘gs.def.list’
pipeline.htmlGroupSummary: no visible binding for global variable
‘group.labels’
pipeline.htmlGroupSummary: no visible binding for global variable
‘files.name’
pipeline.htmlGroupSummary: no visible binding for global variable
‘preferences’
pipeline.htmlGroupSummary: no visible binding for global variable
‘indata’
pipeline.htmlModuleSummary: no visible binding for global variable
‘files.name’
pipeline.htmlModuleSummary: no visible binding for global variable
‘group.labels’
pipeline.htmlModuleSummary: no visible binding for global variable
‘spot.list.overexpression’
pipeline.htmlModuleSummary: no visible binding for global variable
‘spot.list.group.overexpression’
pipeline.htmlModuleSummary: no visible binding for global variable
‘spot.list.kmeans’
pipeline.htmlModuleSummary: no visible binding for global variable
‘spot.list.dmap’
pipeline.htmlSampleSummary: no visible binding for global variable
‘indata’
pipeline.htmlSampleSummary: no visible binding for global variable
‘files.name’
pipeline.htmlSampleSummary: no visible binding for global variable
‘group.labels’
pipeline.htmlSummary: no visible binding for global variable
‘files.name’
pipeline.htmlSummary: no visible binding for global variable ‘indata’
pipeline.htmlSummary: no visible binding for global variable
‘group.labels’
pipeline.htmlSummary: no visible binding for global variable
‘preferences’
pipeline.moduleCorrelationMap: no visible global function definition
for ‘quantile’
pipeline.moduleCorrelationMap: no visible global function definition
for ‘layout’
pipeline.moduleCorrelationMap: no visible global function definition
for ‘par’
pipeline.moduleCorrelationMap: no visible global function definition
for ‘image’
pipeline.moduleCorrelationMap: no visible binding for global variable
‘group.colors’
pipeline.moduleCorrelationMap: no visible global function definition
for ‘color.palette.heatmaps’
pipeline.moduleCorrelationMap: no visible global function definition
for ‘box’
pipeline.moduleCorrelationMap : <anonymous>: no visible global function
definition for ‘rect’
pipeline.moduleCorrelationMap: no visible binding for global variable
‘preferences’
pipeline.moduleCorrelationMap : <anonymous>: no visible global function
definition for ‘sd’
pipeline.moduleCorrelationMap : <anonymous>: no visible global function
definition for ‘text’
pipeline.moduleCorrelationMap: no visible global function definition
for ‘as.dendrogram’
pipeline.moduleCorrelationMap: no visible global function definition
for ‘plot’
pipeline.moduleCorrelationMap: no visible global function definition
for ‘title’
pipeline.patAssignment: no visible binding for global variable
‘preferences’
pipeline.patAssignment: no visible global function definition for ‘sd’
pipeline.patAssignment: no visible binding for '<<-' assignment to
‘pat.labels’
pipeline.patAssignment: no visible binding for global variable
‘pat.labels’
pipeline.prepareAnnotation: no visible binding for global variable
‘indata’
pipeline.prepareAnnotation: no visible binding for '<<-' assignment to
‘gene.info’
pipeline.prepareAnnotation: no visible binding for '<<-' assignment to
‘chromosome.list’
pipeline.prepareAnnotation: no visible binding for '<<-' assignment to
‘preferences’
pipeline.prepareAnnotation: no visible binding for global variable
‘preferences’
pipeline.prepareAnnotation: no visible binding for global variable
‘gene.info’
pipeline.prepareAnnotation: no visible binding for global variable
‘chromosome.list’
pipeline.prepareAnnotation: no visible binding for '<<-' assignment to
‘unique.protein.ids’
pipeline.prepareAnnotation: no visible binding for global variable
‘unique.protein.ids’
pipeline.prepareAnnotation: no visible binding for '<<-' assignment to
‘gs.def.list’
pipeline.prepareAnnotation: no visible binding for global variable
‘gs.def.list’
pipeline.prepareAnnotation: no visible binding for global variable
‘head’
pipeline.prepareAnnotation : <anonymous>: no visible binding for global
variable ‘gene.info’
pipeline.prepareAnnotation: no visible global function definition for
‘data’
pipeline.prepareAnnotation: no visible binding for global variable
‘opossom.genesets’
pipeline.prepareAnnotation : <anonymous>: no visible binding for global
variable ‘unique.protein.ids’
pipeline.prepareIndata: no visible binding for '<<-' assignment to
‘indata.sample.mean’
pipeline.prepareIndata: no visible binding for global variable ‘indata’
pipeline.prepareIndata: no visible binding for global variable
‘preferences’
pipeline.prepareIndata: no visible binding for '<<-' assignment to
‘indata’
pipeline.prepareIndata: no visible binding for '<<-' assignment to
‘group.labels’
pipeline.prepareIndata: no visible binding for global variable
‘group.labels’
pipeline.prepareIndata: no visible binding for '<<-' assignment to
‘group.colors’
pipeline.prepareIndata: no visible binding for global variable
‘group.colors’
pipeline.prepareIndata: no visible binding for '<<-' assignment to
‘indata.gene.mean’
pipeline.prepareIndata: no visible binding for global variable
‘indata.gene.mean’
pipeline.qualityCheck: no visible binding for global variable
‘files.name’
pipeline.qualityCheck : plot.poly.density: no visible binding for
global variable ‘indata’
pipeline.qualityCheck : plot.poly.density: no visible global function
definition for ‘par’
pipeline.qualityCheck : plot.poly.density: no visible global function
definition for ‘plot’
pipeline.qualityCheck : plot.poly.density: no visible global function
definition for ‘lines’
pipeline.qualityCheck : plot.poly.density: no visible global function
definition for ‘polygon’
pipeline.qualityCheck : plot.poly.density: no visible binding for
global variable ‘sd’
pipeline.qualityCheck: no visible binding for global variable ‘indata’
pipeline.qualityCheck : <anonymous>: no visible global function
definition for ‘density’
pipeline.qualityCheck: no visible global function definition for ‘pdf’
pipeline.qualityCheck: no visible global function definition for ‘par’
pipeline.qualityCheck: no visible global function definition for ‘plot’
pipeline.qualityCheck: no visible binding for global variable ‘lines’
pipeline.qualityCheck: no visible binding for global variable
‘group.labels’
pipeline.qualityCheck: no visible binding for global variable
‘groupwise.group.colors’
pipeline.qualityCheck: no visible binding for global variable ‘sd’
pipeline.qualityCheck: no visible global function definition for
‘quantile’
pipeline.qualityCheck: no visible binding for global variable
‘group.colors’
pipeline.qualityCheck: no visible global function definition for
‘abline’
pipeline.qualityCheck: no visible global function definition for
‘legend’
pipeline.qualityCheck: no visible global function definition for ‘text’
pipeline.qualityCheck: no visible global function definition for
‘barplot’
pipeline.qualityCheck: no visible global function definition for ‘box’
pipeline.qualityCheck: no visible global function definition for
‘boxplot’
pipeline.qualityCheck: no visible global function definition for ‘axis’
pipeline.qualityCheck: no visible global function definition for
‘dev.off’
pipeline.sampleExpressionPortraits: no visible binding for global
variable ‘files.name’
pipeline.sampleExpressionPortraits: no visible global function
definition for ‘pdf’
pipeline.sampleExpressionPortraits: no visible global function
definition for ‘par’
pipeline.sampleExpressionPortraits: no visible binding for global
variable ‘group.labels’
pipeline.sampleExpressionPortraits: no visible global function
definition for ‘plot’
pipeline.sampleExpressionPortraits: no visible global function
definition for ‘mtext’
pipeline.sampleExpressionPortraits: no visible binding for global
variable ‘groupwise.group.colors’
pipeline.sampleExpressionPortraits: no visible global function
definition for ‘image’
pipeline.sampleExpressionPortraits: no visible binding for global
variable ‘metadata’
pipeline.sampleExpressionPortraits: no visible binding for global
variable ‘preferences’
pipeline.sampleExpressionPortraits: no visible global function
definition for ‘color.palette.portraits’
pipeline.sampleExpressionPortraits: no visible global function
definition for ‘title’
pipeline.sampleExpressionPortraits: no visible binding for global
variable ‘indata’
pipeline.sampleExpressionPortraits: no visible binding for global
variable ‘group.silhouette.coef’
pipeline.sampleExpressionPortraits: no visible global function
definition for ‘box’
pipeline.sampleExpressionPortraits: no visible global function
definition for ‘persp’
pipeline.sampleExpressionPortraits: no visible global function
definition for ‘dev.off’
pipeline.sampleExpressionPortraits: no visible global function
definition for ‘text’
pipeline.sampleSimilarityAnalysisCor: no visible global function
definition for ‘col2rgb’
pipeline.sampleSimilarityAnalysisCor: no visible binding for global
variable ‘groupwise.group.colors’
pipeline.sampleSimilarityAnalysisCor : <anonymous>: no visible global
function definition for ‘rgb’
pipeline.sampleSimilarityAnalysisCor: no visible binding for global
variable ‘group.colors’
pipeline.sampleSimilarityAnalysisCor: no visible binding for global
variable ‘group.silhouette.coef’
pipeline.sampleSimilarityAnalysisCor: no visible binding for global
variable ‘group.labels’
pipeline.sampleSimilarityAnalysisCor: no visible global function
definition for ‘cor’
pipeline.sampleSimilarityAnalysisCor: no visible binding for global
variable ‘preferences’
pipeline.sampleSimilarityAnalysisCor: no visible binding for global
variable ‘metadata’
pipeline.sampleSimilarityAnalysisCor: no visible binding for global
variable ‘files.name’
pipeline.sampleSimilarityAnalysisCor: no visible global function
definition for ‘pdf’
pipeline.sampleSimilarityAnalysisCor: no visible global function
definition for ‘par’
pipeline.sampleSimilarityAnalysisCor: no visible global function
definition for ‘plot’
pipeline.sampleSimilarityAnalysisCor: no visible global function
definition for ‘legend’
pipeline.sampleSimilarityAnalysisCor: no visible global function
definition for ‘box’
pipeline.sampleSimilarityAnalysisCor: no visible global function
definition for ‘dev.off’
pipeline.sampleSimilarityAnalysisCor: no visible global function
definition for ‘hclust’
pipeline.sampleSimilarityAnalysisCor: no visible global function
definition for ‘dist’
pipeline.sampleSimilarityAnalysisCor: no visible global function
definition for ‘color.palette.heatmaps’
pipeline.sampleSimilarityAnalysisCor: no visible global function
definition for ‘image’
pipeline.sampleSimilarityAnalysisCor: no visible global function
definition for ‘axis’
pipeline.sampleSimilarityAnalysisCor : <anonymous>: no visible binding
for global variable ‘group.labels’
pipeline.sampleSimilarityAnalysisCor : <anonymous>: no visible global
function definition for ‘hclust’
pipeline.sampleSimilarityAnalysisCor : <anonymous>: no visible global
function definition for ‘dist’
pipeline.sampleSimilarityAnalysisCor: no visible global function
definition for ‘as.dendrogram’
pipeline.sampleSimilarityAnalysisED: no visible binding for global
variable ‘files.name’
pipeline.sampleSimilarityAnalysisED: no visible global function
definition for ‘pdf’
pipeline.sampleSimilarityAnalysisED: no visible binding for global
variable ‘preferences’
pipeline.sampleSimilarityAnalysisED: no visible binding for global
variable ‘metadata’
pipeline.sampleSimilarityAnalysisED: no visible global function
definition for ‘par’
pipeline.sampleSimilarityAnalysisED: no visible global function
definition for ‘plot’
pipeline.sampleSimilarityAnalysisED: no visible binding for global
variable ‘group.colors’
pipeline.sampleSimilarityAnalysisED: no visible global function
definition for ‘title’
pipeline.sampleSimilarityAnalysisED: no visible global function
definition for ‘legend’
pipeline.sampleSimilarityAnalysisED: no visible binding for global
variable ‘group.labels’
pipeline.sampleSimilarityAnalysisED: no visible binding for global
variable ‘groupwise.group.colors’
pipeline.sampleSimilarityAnalysisED: no visible global function
definition for ‘dev.off’
pipeline.sampleSimilarityAnalysisED: no visible global function
definition for ‘dist’
pipeline.sampleSimilarityAnalysisED: no visible global function
definition for ‘box’
pipeline.sampleSimilarityAnalysisED: no visible global function
definition for ‘color.palette.heatmaps’
pipeline.sampleSimilarityAnalysisED: no visible global function
definition for ‘image’
pipeline.sampleSimilarityAnalysisED: no visible global function
definition for ‘axis’
pipeline.sampleSimilarityAnalysisICA: no visible binding for global
variable ‘files.name’
pipeline.sampleSimilarityAnalysisICA: no visible global function
definition for ‘pdf’
pipeline.sampleSimilarityAnalysisICA: no visible binding for global
variable ‘preferences’
pipeline.sampleSimilarityAnalysisICA: no visible binding for global
variable ‘metadata’
pipeline.sampleSimilarityAnalysisICA: no visible global function
definition for ‘layout’
pipeline.sampleSimilarityAnalysisICA: no visible global function
definition for ‘par’
pipeline.sampleSimilarityAnalysisICA: no visible binding for global
variable ‘group.colors’
pipeline.sampleSimilarityAnalysisICA: no visible global function
definition for ‘plot’
pipeline.sampleSimilarityAnalysisICA: no visible global function
definition for ‘text’
pipeline.sampleSimilarityAnalysisICA: no visible global function
definition for ‘mtext’
pipeline.sampleSimilarityAnalysisICA: no visible global function
definition for ‘legend’
pipeline.sampleSimilarityAnalysisICA: no visible binding for global
variable ‘group.labels’
pipeline.sampleSimilarityAnalysisICA: no visible binding for global
variable ‘groupwise.group.colors’
pipeline.sampleSimilarityAnalysisICA: no visible global function
definition for ‘points’
pipeline.sampleSimilarityAnalysisICA: no visible global function
definition for ‘box’
pipeline.sampleSimilarityAnalysisICA: no visible binding for global
variable ‘indata’
pipeline.sampleSimilarityAnalysisICA: no visible global function
definition for ‘dev.off’
pipeline.sampleSimilarityAnalysisSOM: no visible binding for global
variable ‘files.name’
pipeline.sampleSimilarityAnalysisSOM: no visible global function
definition for ‘pdf’
pipeline.sampleSimilarityAnalysisSOM: no visible binding for global
variable ‘preferences’
pipeline.sampleSimilarityAnalysisSOM: no visible binding for global
variable ‘metadata’
pipeline.sampleSimilarityAnalysisSOM: no visible global function
definition for ‘par’
pipeline.sampleSimilarityAnalysisSOM: no visible global function
definition for ‘plot’
pipeline.sampleSimilarityAnalysisSOM: no visible binding for global
variable ‘group.labels’
pipeline.sampleSimilarityAnalysisSOM: no visible global function
definition for ‘legend’
pipeline.sampleSimilarityAnalysisSOM: no visible binding for global
variable ‘groupwise.group.colors’
pipeline.sampleSimilarityAnalysisSOM: no visible global function
definition for ‘points’
pipeline.sampleSimilarityAnalysisSOM: no visible binding for global
variable ‘group.colors’
pipeline.sampleSimilarityAnalysisSOM: no visible global function
definition for ‘box’
pipeline.sampleSimilarityAnalysisSOM: no visible global function
definition for ‘text’
pipeline.sampleSimilarityAnalysisSOM: no visible binding for global
variable ‘indata’
pipeline.sampleSimilarityAnalysisSOM: no visible global function
definition for ‘chull’
pipeline.sampleSimilarityAnalysisSOM: no visible global function
definition for ‘polygon’
pipeline.sampleSimilarityAnalysisSOM: no visible global function
definition for ‘color.palette.portraits’
pipeline.sampleSimilarityAnalysisSOM: no visible global function
definition for ‘dev.off’
pipeline.summarySheetsGroups: no visible binding for global variable
‘metadata’
pipeline.summarySheetsGroups: no visible binding for global variable
‘group.labels’
pipeline.summarySheetsGroups : <anonymous>: no visible binding for
global variable ‘sd’
pipeline.summarySheetsGroups: no visible binding for global variable
‘files.name’
pipeline.summarySheetsGroups: no visible global function definition for
‘pdf’
pipeline.summarySheetsGroups: no visible global function definition for
‘par’
pipeline.summarySheetsGroups: no visible global function definition for
‘plot’
pipeline.summarySheetsGroups: no visible global function definition for
‘mtext’
pipeline.summarySheetsGroups: no visible binding for global variable
‘groupwise.group.colors’
pipeline.summarySheetsGroups: no visible global function definition for
‘image’
pipeline.summarySheetsGroups: no visible binding for global variable
‘preferences’
pipeline.summarySheetsGroups: no visible global function definition for
‘color.palette.portraits’
pipeline.summarySheetsGroups: no visible global function definition for
‘title’
pipeline.summarySheetsGroups: no visible global function definition for
‘box’
pipeline.summarySheetsGroups: no visible global function definition for
‘layout’
pipeline.summarySheetsGroups: no visible global function definition for
‘text’
pipeline.summarySheetsGroups: no visible global function definition for
‘colorRampPalette’
pipeline.summarySheetsGroups: no visible global function definition for
‘axis’
pipeline.summarySheetsGroups: no visible global function definition for
‘ecdf’
pipeline.summarySheetsGroups: no visible global function definition for
‘dev.off’
pipeline.summarySheetsGroups: no visible binding for global variable
‘group.silhouette.coef’
pipeline.summarySheetsGroups: no visible global function definition for
‘cor’
pipeline.summarySheetsGroups : <anonymous>: no visible binding for
global variable ‘group.labels’
pipeline.summarySheetsGroups: no visible binding for global variable
‘indata’
pipeline.summarySheetsGroups: no visible global function definition for
‘barplot’
pipeline.summarySheetsGroups: no visible binding for global variable
‘group.colors’
pipeline.summarySheetsGroups: no visible global function definition for
‘abline’
pipeline.summarySheetsGroups: no visible global function definition for
‘points’
pipeline.summarySheetsGroups: no visible global function definition for
‘boxplot’
pipeline.summarySheetsGroups : <anonymous>: no visible global function
definition for ‘axis’
pipeline.summarySheetsGroups : <anonymous>: no visible binding for
global variable ‘groupwise.group.colors’
pipeline.summarySheetsGroups: no visible global function definition for
‘hclust’
pipeline.summarySheetsGroups: no visible global function definition for
‘dist’
pipeline.summarySheetsGroups: no visible global function definition for
‘cutree’
pipeline.summarySheetsGroups: no visible global function definition for
‘quantile’
pipeline.summarySheetsGroups: no visible global function definition for
‘rect’
pipeline.summarySheetsModules: no visible binding for global variable
‘files.name’
pipeline.summarySheetsModules: no visible binding for global variable
‘spot.list.overexpression’
pipeline.summarySheetsModules: no visible binding for global variable
‘spot.list.underexpression’
pipeline.summarySheetsModules: no visible binding for global variable
‘spot.list.correlation’
pipeline.summarySheetsModules: no visible binding for global variable
‘spot.list.kmeans’
pipeline.summarySheetsModules: no visible binding for global variable
‘spot.list.dmap’
pipeline.summarySheetsModules: no visible binding for global variable
‘group.labels’
pipeline.summarySheetsModules: no visible binding for global variable
‘spot.list.group.overexpression’
pipeline.summarySheetsModules: no visible binding for global variable
‘output.paths’
pipeline.summarySheetsPATs: no visible binding for global variable
‘files.name’
pipeline.summarySheetsPATs: no visible binding for global variable
‘metadata’
pipeline.summarySheetsPATs: no visible binding for global variable
‘pat.labels’
pipeline.summarySheetsPATs: no visible global function definition for
‘pdf’
pipeline.summarySheetsPATs: no visible global function definition for
‘hclust’
pipeline.summarySheetsPATs: no visible global function definition for
‘dist’
pipeline.summarySheetsPATs: no visible global function definition for
‘par’
pipeline.summarySheetsPATs: no visible global function definition for
‘plot’
pipeline.summarySheetsPATs: no visible global function definition for
‘frame’
pipeline.summarySheetsPATs: no visible binding for global variable
‘preferences’
pipeline.summarySheetsPATs: no visible global function definition for
‘color.palette.portraits’
pipeline.summarySheetsPATs: no visible global function definition for
‘layout’
pipeline.summarySheetsPATs: no visible global function definition for
‘text’
pipeline.summarySheetsPATs: no visible global function definition for
‘image’
pipeline.summarySheetsPATs: no visible global function definition for
‘box’
pipeline.summarySheetsPATs: no visible binding for global variable
‘group.labels’
pipeline.summarySheetsPATs: no visible global function definition for
‘pie’
pipeline.summarySheetsPATs: no visible binding for global variable
‘groupwise.group.colors’
pipeline.summarySheetsPATs: no visible global function definition for
‘mtext’
pipeline.summarySheetsPATs : <anonymous>: no visible binding for global
variable ‘group.labels’
pipeline.summarySheetsPATs: no visible global function definition for
‘barplot’
pipeline.summarySheetsPATs: no visible global function definition for
‘legend’
pipeline.summarySheetsPATs : <anonymous>: no visible binding for global
variable ‘pat.labels’
pipeline.summarySheetsPATs: no visible global function definition for
‘dev.off’
pipeline.summarySheetsSamples: no visible binding for global variable
‘indata’
pipeline.summarySheetsSamples: no visible binding for global variable
‘output.paths’
pipeline.summarySheetsSamples: no visible binding for global variable
‘preferences’
pipeline.summarySheetsSamples: no visible binding for global variable
‘gs.def.list’
pipeline.summarySheetsSamples: no visible binding for global variable
‘gene.info’
pipeline.summarySheetsSamples: no visible global function definition
for ‘hist’
pipeline.summarySheetsSamples: no visible binding for global variable
‘p.g.m’
pipeline.summarySheetsSamples: no visible global function definition
for ‘pdf’
pipeline.summarySheetsSamples: no visible global function definition
for ‘layout’
pipeline.summarySheetsSamples: no visible global function definition
for ‘par’
pipeline.summarySheetsSamples: no visible global function definition
for ‘plot’
pipeline.summarySheetsSamples: no visible global function definition
for ‘text’
pipeline.summarySheetsSamples: no visible binding for global variable
‘perc.DE.m’
pipeline.summarySheetsSamples: no visible binding for global variable
‘fdr.g.m’
pipeline.summarySheetsSamples: no visible binding for global variable
‘t.g.m’
pipeline.summarySheetsSamples: no visible global function definition
for ‘image’
pipeline.summarySheetsSamples: no visible binding for global variable
‘metadata’
pipeline.summarySheetsSamples: no visible global function definition
for ‘color.palette.portraits’
pipeline.summarySheetsSamples: no visible global function definition
for ‘axis’
pipeline.summarySheetsSamples: no visible global function definition
for ‘box’
pipeline.summarySheetsSamples: no visible global function definition
for ‘rect’
pipeline.summarySheetsSamples: no visible global function definition
for ‘mtext’
pipeline.summarySheetsSamples: no visible global function definition
for ‘abline’
pipeline.summarySheetsSamples: no visible binding for global variable
‘n.0.m’
pipeline.summarySheetsSamples: no visible global function definition
for ‘lines’
pipeline.summarySheetsSamples: no visible binding for global variable
‘Fdr.g.m’
pipeline.summarySheetsSamples: no visible global function definition
for ‘legend’
pipeline.summarySheetsSamples: no visible binding for global variable
‘spot.list.samples’
pipeline.summarySheetsSamples: no visible global function definition
for ‘dev.off’
pipeline.supportingMaps: no visible binding for global variable
‘files.name’
pipeline.supportingMaps: no visible global function definition for
‘pdf’
pipeline.supportingMaps: no visible global function definition for
‘par’
pipeline.supportingMaps: no visible binding for global variable
‘som.result’
pipeline.supportingMaps: no visible global function definition for
‘image’
pipeline.supportingMaps: no visible binding for global variable
‘preferences’
pipeline.supportingMaps: no visible global function definition for
‘color.palette.heatmaps’
pipeline.supportingMaps: no visible global function definition for
‘mtext’
pipeline.supportingMaps: no visible global function definition for
‘box’
pipeline.supportingMaps: no visible global function definition for
‘layout’
pipeline.supportingMaps: no visible global function definition for
‘axis’
pipeline.supportingMaps: no visible binding for global variable
‘metadata’
pipeline.supportingMaps: no visible binding for global variable ‘var’
pipeline.supportingMaps: no visible binding for global variable ‘p.m’
pipeline.supportingMaps: no visible global function definition for
‘colorRampPalette’
pipeline.supportingMaps: no visible global function definition for
‘quantile’
pipeline.supportingMaps : <anonymous>: no visible global function
definition for ‘hist’
pipeline.supportingMaps : <anonymous>: no visible binding for global
variable ‘indata’
pipeline.supportingMaps: no visible global function definition for
‘cor’
pipeline.supportingMaps: no visible binding for global variable
‘indata’
pipeline.supportingMaps : <anonymous>: no visible binding for global
variable ‘metadata’
pipeline.supportingMaps : <anonymous>: no visible binding for global
variable ‘preferences’
pipeline.supportingMaps: no visible global function definition for
‘dev.off’
pipeline.topologyProfiles: no visible binding for global variable
‘metadata’
pipeline.topologyProfiles: no visible binding for global variable
‘files.name’
pipeline.topologyProfiles: no visible binding for global variable
‘group.labels’
pipeline.topologyProfiles: no visible global function definition for
‘pdf’
pipeline.topologyProfiles: no visible global function definition for
‘par’
pipeline.topologyProfiles: no visible binding for global variable
‘preferences’
pipeline.topologyProfiles: no visible global function definition for
‘sd’
pipeline.topologyProfiles: no visible global function definition for
‘barplot’
pipeline.topologyProfiles: no visible binding for global variable
‘group.colors’
pipeline.topologyProfiles: no visible binding for global variable
‘indata’
pipeline.topologyProfiles: no visible global function definition for
‘box’
pipeline.topologyProfiles: no visible global function definition for
‘boxplot’
pipeline.topologyProfiles: no visible binding for global variable
‘groupwise.group.colors’
pipeline.topologyProfiles: no visible global function definition for
‘axis’
pipeline.topologyProfiles : <anonymous>: no visible binding for global
variable ‘group.labels’
pipeline.topologyProfiles : <anonymous>: no visible binding for global
variable ‘preferences’
pipeline.topologyProfiles: no visible global function definition for
‘dev.off’
radarchart: no visible global function definition for ‘plot’
radarchart: no visible global function definition for ‘polygon’
radarchart: no visible global function definition for ‘text’
radarchart: no visible global function definition for ‘arrows’
radarchart: no visible global function definition for ‘points’
util.cat: no visible global function definition for ‘flush.console’
Undefined global functions or variables:
Fdr.g.m WAD.g.m abline add_edges aov arrows as as.dendrogram axis
barplot box boxplot chromosome.list chull col2rgb
color.palette.heatmaps color.palette.portraits colorRampPalette combn
cor cutree data density dev.off dist ecdf env fdr.g.m files.name
fisher.test flush.console frame gene.info graph.empty group.colors
group.labels group.silhouette.coef groupwise.group.colors gs.def.list
hclust head hist image indata indata.gene.mean indata.sample.mean
kmeans layout legend lines metadata modifyList mtext n.0.m na.omit
opossom.genesets order.dendrogram output.paths p.g.m p.m par
pat.labels pbeta pdf perc.DE.m persp pie plot points polygon
preferences pt quantile rect reorder rgb samples.GSZ.scores sd
sessionInfo som.result spot.list.correlation spot.list.dmap
spot.list.group.overexpression spot.list.kmeans
spot.list.overexpression spot.list.samples spot.list.underexpression
t.ensID.m t.g.m t.m text title unique.protein.ids v var wilcox.test
write.csv2
Consider adding
importFrom("grDevices", "chull", "col2rgb", "colorRampPalette",
"dev.off", "pdf", "rgb")
importFrom("graphics", "abline", "arrows", "axis", "barplot", "box",
"boxplot", "frame", "hist", "image", "layout", "legend",
"lines", "mtext", "par", "persp", "pie", "plot", "points",
"polygon", "rect", "text", "title")
importFrom("methods", "as")
importFrom("stats", "aov", "as.dendrogram", "cor", "cutree", "density",
"dist", "ecdf", "fisher.test", "hclust", "kmeans",
"na.omit", "order.dendrogram", "pbeta", "pt", "quantile",
"reorder", "sd", "var", "wilcox.test")
importFrom("utils", "combn", "data", "flush.console", "head",
"modifyList", "sessionInfo", "write.csv2")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
oposSOM-package 25.504 0.264 52.155
opossom.run 9.076 0.228 31.433
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.6-bioc/meat/oposSOM.Rcheck/00check.log’
for details.
Installation output
oposSOM.Rcheck/00install.out
Tests output
Example timings
oposSOM.Rcheck/oposSOM-Ex.timings