oposSOM 1.10.0
Henry Loeffler-Wirth
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/oposSOM | | Last Changed Rev: 117079 / Revision: 122332 | | Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings oposSOM_1.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/oposSOM.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘oposSOM/DESCRIPTION’ ... OK
* this is package ‘oposSOM’ version ‘1.10.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘oposSOM’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘grDevices:::.smoothScatterCalcDensity’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GeneSet.Fisher : fn: no visible global function definition for
‘fisher.test’
GeneSet.Fisher: no visible global function definition for ‘parSapply’
get.beta.statistic: no visible global function definition for ‘pbeta’
heatmap: no visible binding for global variable ‘dist’
heatmap: no visible binding for global variable ‘hclust’
heatmap : <anonymous>: no visible global function definition for
‘reorder’
heatmap: no visible global function definition for ‘as.dendrogram’
heatmap: no visible global function definition for ‘order.dendrogram’
heatmap: no visible binding for global variable ‘sd’
heatmap: no visible global function definition for ‘par’
heatmap: no visible global function definition for ‘layout’
heatmap: no visible global function definition for ‘image’
heatmap: no visible global function definition for ‘axis’
heatmap: no visible global function definition for ‘mtext’
heatmap: no visible global function definition for ‘frame’
heatmap: no visible global function definition for ‘title’
opossom.new: no visible global function definition for ‘modifyList’
opossom.run: no visible global function definition for ‘sessionInfo’
pipeline.2ndLvlComponentAnalysis: no visible binding for global
variable ‘files.name’
pipeline.2ndLvlComponentAnalysis: no visible global function definition
for ‘pdf’
pipeline.2ndLvlComponentAnalysis: no visible binding for global
variable ‘metagene.filter.list’
pipeline.2ndLvlComponentAnalysis: no visible binding for global
variable ‘metadata’
pipeline.2ndLvlComponentAnalysis: no visible global function definition
for ‘layout’
pipeline.2ndLvlComponentAnalysis: no visible global function definition
for ‘par’
pipeline.2ndLvlComponentAnalysis: no visible binding for global
variable ‘group.colors’
pipeline.2ndLvlComponentAnalysis: no visible global function definition
for ‘text’
pipeline.2ndLvlComponentAnalysis: no visible global function definition
for ‘mtext’
pipeline.2ndLvlComponentAnalysis: no visible global function definition
for ‘legend’
pipeline.2ndLvlComponentAnalysis: no visible binding for global
variable ‘group.labels’
pipeline.2ndLvlComponentAnalysis: no visible binding for global
variable ‘groupwise.group.colors’
pipeline.2ndLvlComponentAnalysis: no visible global function definition
for ‘points’
pipeline.2ndLvlComponentAnalysis: no visible global function definition
for ‘box’
pipeline.2ndLvlComponentAnalysis: no visible binding for global
variable ‘indata’
pipeline.2ndLvlComponentAnalysis: no visible global function definition
for ‘dev.off’
pipeline.2ndLvlCorrelationAnalysis: no visible global function
definition for ‘col2rgb’
pipeline.2ndLvlCorrelationAnalysis: no visible binding for global
variable ‘groupwise.group.colors’
pipeline.2ndLvlCorrelationAnalysis : <anonymous>: no visible global
function definition for ‘rgb’
pipeline.2ndLvlCorrelationAnalysis: no visible binding for global
variable ‘group.colors’
pipeline.2ndLvlCorrelationAnalysis: no visible binding for global
variable ‘group.silhouette.coef’
pipeline.2ndLvlCorrelationAnalysis: no visible binding for global
variable ‘group.labels’
pipeline.2ndLvlCorrelationAnalysis: no visible binding for global
variable ‘files.name’
pipeline.2ndLvlCorrelationAnalysis: no visible global function
definition for ‘pdf’
pipeline.2ndLvlCorrelationAnalysis: no visible binding for global
variable ‘metagene.filter.list’
pipeline.2ndLvlCorrelationAnalysis: no visible binding for global
variable ‘metadata’
pipeline.2ndLvlCorrelationAnalysis: no visible global function
definition for ‘cor’
pipeline.2ndLvlCorrelationAnalysis: no visible global function
definition for ‘par’
pipeline.2ndLvlCorrelationAnalysis: no visible binding for global
variable ‘indata’
pipeline.2ndLvlCorrelationAnalysis: no visible global function
definition for ‘legend’
pipeline.2ndLvlCorrelationAnalysis: no visible global function
definition for ‘box’
pipeline.2ndLvlCorrelationAnalysis: no visible global function
definition for ‘hclust’
pipeline.2ndLvlCorrelationAnalysis: no visible global function
definition for ‘dist’
pipeline.2ndLvlCorrelationAnalysis: no visible global function
definition for ‘as.dendrogram’
pipeline.2ndLvlCorrelationAnalysis: no visible global function
definition for ‘color.palette.heatmaps’
pipeline.2ndLvlCorrelationAnalysis: no visible global function
definition for ‘image’
pipeline.2ndLvlCorrelationAnalysis: no visible global function
definition for ‘axis’
pipeline.2ndLvlCorrelationAnalysis : <anonymous>: no visible binding
for global variable ‘group.labels’
pipeline.2ndLvlCorrelationAnalysis : <anonymous>: no visible global
function definition for ‘hclust’
pipeline.2ndLvlCorrelationAnalysis : <anonymous>: no visible global
function definition for ‘dist’
pipeline.2ndLvlCorrelationAnalysis: no visible global function
definition for ‘dev.off’
pipeline.2ndLvlModuleCorrelation: no visible global function definition
for ‘cor’
pipeline.2ndLvlModuleCorrelation: no visible global function definition
for ‘quantile’
pipeline.2ndLvlModuleCorrelation: no visible binding for global
variable ‘indata’
pipeline.2ndLvlModuleCorrelation: no visible global function definition
for ‘layout’
pipeline.2ndLvlModuleCorrelation: no visible global function definition
for ‘par’
pipeline.2ndLvlModuleCorrelation: no visible global function definition
for ‘image’
pipeline.2ndLvlModuleCorrelation: no visible binding for global
variable ‘group.colors’
pipeline.2ndLvlModuleCorrelation: no visible global function definition
for ‘color.palette.heatmaps’
pipeline.2ndLvlModuleCorrelation: no visible global function definition
for ‘box’
pipeline.2ndLvlModuleCorrelation : <anonymous>: no visible global
function definition for ‘rect’
pipeline.2ndLvlModuleCorrelation: no visible binding for global
variable ‘preferences’
pipeline.2ndLvlModuleCorrelation : <anonymous>: no visible global
function definition for ‘sd’
pipeline.2ndLvlModuleCorrelation : <anonymous>: no visible global
function definition for ‘text’
pipeline.2ndLvlModuleCorrelation: no visible global function definition
for ‘as.dendrogram’
pipeline.2ndLvlModuleCorrelation: no visible global function definition
for ‘title’
pipeline.2ndLvlSimilarityAnalysis: no visible binding for '<<-'
assignment to ‘metagene.filter.list’
pipeline.2ndLvlSimilarityAnalysis: no visible binding for global
variable ‘metagene.filter.list’
pipeline.2ndLvlSimilarityAnalysis: no visible binding for global
variable ‘preferences’
pipeline.2ndLvlSimilarityAnalysis: no visible binding for global
variable ‘metadata’
pipeline.2ndLvlSimilarityAnalysis: no visible binding for global
variable ‘var’
pipeline.2ndLvlSimilarityAnalysis: no visible binding for global
variable ‘files.name’
pipeline.2ndLvlSimilarityAnalysis: no visible global function
definition for ‘pdf’
pipeline.2ndLvlSimilarityAnalysis: no visible global function
definition for ‘par’
pipeline.2ndLvlSimilarityAnalysis: no visible global function
definition for ‘dist’
pipeline.2ndLvlSimilarityAnalysis: no visible binding for global
variable ‘indata’
pipeline.2ndLvlSimilarityAnalysis: no visible binding for global
variable ‘group.colors’
pipeline.2ndLvlSimilarityAnalysis: no visible global function
definition for ‘title’
pipeline.2ndLvlSimilarityAnalysis: no visible global function
definition for ‘box’
pipeline.2ndLvlSimilarityAnalysis: no visible global function
definition for ‘legend’
pipeline.2ndLvlSimilarityAnalysis: no visible binding for global
variable ‘group.labels’
pipeline.2ndLvlSimilarityAnalysis: no visible binding for global
variable ‘groupwise.group.colors’
pipeline.2ndLvlSimilarityAnalysis: no visible global function
definition for ‘color.palette.heatmaps’
pipeline.2ndLvlSimilarityAnalysis: no visible global function
definition for ‘image’
pipeline.2ndLvlSimilarityAnalysis: no visible global function
definition for ‘axis’
pipeline.2ndLvlSimilarityAnalysis: no visible global function
definition for ‘dev.off’
pipeline.2ndLvlSom: no visible binding for '<<-' assignment to
‘secLvlSom.custom’
pipeline.2ndLvlSom: no visible binding for global variable ‘metadata’
pipeline.2ndLvlSom: no visible binding for global variable
‘preferences’
pipeline.2ndLvlSom: no visible binding for '<<-' assignment to
‘secLvlSom.20.20’
pipeline.2ndLvlSom: no visible binding for global variable
‘secLvlSom.custom’
pipeline.2ndLvlSom: no visible binding for global variable ‘files.name’
pipeline.2ndLvlSom: no visible global function definition for ‘pdf’
pipeline.2ndLvlSom: no visible global function definition for ‘par’
pipeline.2ndLvlSom: no visible binding for global variable
‘group.labels’
pipeline.2ndLvlSom: no visible global function definition for ‘legend’
pipeline.2ndLvlSom: no visible binding for global variable
‘groupwise.group.colors’
pipeline.2ndLvlSom: no visible global function definition for ‘points’
pipeline.2ndLvlSom: no visible binding for global variable
‘group.colors’
pipeline.2ndLvlSom: no visible global function definition for ‘box’
pipeline.2ndLvlSom: no visible global function definition for ‘text’
pipeline.2ndLvlSom: no visible binding for global variable ‘indata’
pipeline.2ndLvlSom: no visible global function definition for ‘chull’
pipeline.2ndLvlSom: no visible global function definition for ‘polygon’
pipeline.2ndLvlSom: no visible binding for global variable
‘secLvlSom.20.20’
pipeline.2ndLvlSom: no visible global function definition for
‘color.palette.portraits’
pipeline.2ndLvlSom: no visible global function definition for ‘dev.off’
pipeline.3rdLvlChromosomalEnrichment: no visible binding for global
variable ‘output.paths’
pipeline.3rdLvlChromosomalEnrichment: no visible binding for global
variable ‘files.name’
pipeline.3rdLvlChromosomalEnrichment : plot.set.list.chromosomes: no
visible binding for global variable ‘gene.positions’
pipeline.3rdLvlChromosomalEnrichment : plot.set.list.chromosomes: no
visible binding for global variable ‘gene.positions.list’
pipeline.3rdLvlChromosomalEnrichment : plot.set.list.chromosomes: no
visible global function definition for ‘write.csv2’
pipeline.3rdLvlChromosomalEnrichment : plot.set.list.chromosomes: no
visible global function definition for ‘colorRampPalette’
pipeline.3rdLvlChromosomalEnrichment : plot.set.list.chromosomes: no
visible binding for global variable ‘head’
pipeline.3rdLvlChromosomalEnrichment : plot.set.list.chromosomes: no
visible global function definition for ‘par’
pipeline.3rdLvlChromosomalEnrichment : plot.set.list.chromosomes: no
visible global function definition for ‘image’
pipeline.3rdLvlChromosomalEnrichment : plot.set.list.chromosomes: no
visible global function definition for ‘title’
pipeline.3rdLvlChromosomalEnrichment : plot.set.list.chromosomes: no
visible global function definition for ‘box’
pipeline.3rdLvlChromosomalEnrichment : plot.set.list.chromosomes: no
visible global function definition for ‘abline’
pipeline.3rdLvlChromosomalEnrichment : plot.set.list.chromosomes: no
visible global function definition for ‘axis’
pipeline.3rdLvlChromosomalEnrichment : plot.set.list.chromosomes: no
visible global function definition for ‘layout’
pipeline.3rdLvlChromosomalEnrichment : plot.set.list.chromosomes: no
visible global function definition for ‘text’
pipeline.3rdLvlChromosomalEnrichment: no visible global function
definition for ‘pdf’
pipeline.3rdLvlChromosomalEnrichment: no visible binding for global
variable ‘gene.positions.list’
pipeline.3rdLvlChromosomalEnrichment: no visible binding for global
variable ‘spot.list.overexpression’
pipeline.3rdLvlChromosomalEnrichment: no visible global function
definition for ‘dev.off’
pipeline.3rdLvlChromosomalEnrichment: no visible binding for global
variable ‘spot.list.underexpression’
pipeline.3rdLvlChromosomalEnrichment: no visible binding for global
variable ‘spot.list.kmeans’
pipeline.3rdLvlChromosomalEnrichment: no visible binding for global
variable ‘group.labels’
pipeline.3rdLvlChromosomalEnrichment: no visible binding for global
variable ‘spot.list.group.overexpression’
pipeline.3rdLvlChromosomalEnrichment: no visible binding for global
variable ‘spot.list.dmap’
pipeline.3rdLvlNetworks : plot.set.list.networks: no visible global
function definition for ‘sd’
pipeline.3rdLvlNetworks : plot.set.list.networks: no visible binding
for global variable ‘metadata’
pipeline.3rdLvlNetworks : plot.set.list.networks: no visible global
function definition for ‘cor’
pipeline.3rdLvlNetworks : plot.set.list.networks: no visible global
function definition for ‘par’
pipeline.3rdLvlNetworks : plot.set.list.networks: no visible global
function definition for ‘image’
pipeline.3rdLvlNetworks : plot.set.list.networks: no visible binding
for global variable ‘preferences’
pipeline.3rdLvlNetworks : plot.set.list.networks: no visible global
function definition for ‘rect’
pipeline.3rdLvlNetworks : plot.set.list.networks: no visible global
function definition for ‘legend’
pipeline.3rdLvlNetworks: no visible binding for global variable
‘files.name’
pipeline.3rdLvlNetworks: no visible global function definition for
‘pdf’
pipeline.3rdLvlNetworks: no visible binding for global variable
‘spot.list.overexpression’
pipeline.3rdLvlNetworks: no visible global function definition for
‘dev.off’
pipeline.3rdLvlNetworks: no visible binding for global variable
‘spot.list.underexpression’
pipeline.3rdLvlNetworks: no visible binding for global variable
‘spot.list.kmeans’
pipeline.3rdLvlNetworks: no visible binding for global variable
‘group.labels’
pipeline.3rdLvlNetworks: no visible binding for global variable
‘spot.list.group.overexpression’
pipeline.3rdLvlNetworks: no visible binding for global variable
‘spot.list.dmap’
pipeline.3rdLvlSummarySheets : plot.set.list.reports: no visible global
function definition for ‘sd’
pipeline.3rdLvlSummarySheets : plot.set.list.reports: no visible
binding for global variable ‘group.labels’
pipeline.3rdLvlSummarySheets : plot.set.list.reports: no visible global
function definition for ‘hist’
pipeline.3rdLvlSummarySheets : plot.set.list.reports: no visible
binding for global variable ‘metadata’
pipeline.3rdLvlSummarySheets : plot.set.list.reports: no visible global
function definition for ‘par’
pipeline.3rdLvlSummarySheets : plot.set.list.reports: no visible global
function definition for ‘color.palette.portraits’
pipeline.3rdLvlSummarySheets : plot.set.list.reports: no visible global
function definition for ‘colorRampPalette’
pipeline.3rdLvlSummarySheets : plot.set.list.reports: no visible global
function definition for ‘image’
pipeline.3rdLvlSummarySheets : plot.set.list.reports: no visible
binding for global variable ‘preferences’
pipeline.3rdLvlSummarySheets : plot.set.list.reports: no visible global
function definition for ‘box’
pipeline.3rdLvlSummarySheets : plot.set.list.reports: no visible global
function definition for ‘points’
pipeline.3rdLvlSummarySheets : plot.set.list.reports: no visible global
function definition for ‘text’
pipeline.3rdLvlSummarySheets : plot.set.list.reports: no visible global
function definition for ‘layout’
pipeline.3rdLvlSummarySheets : plot.set.list.reports: no visible global
function definition for ‘axis’
pipeline.3rdLvlSummarySheets : plot.set.list.reports: no visible global
function definition for ‘barplot’
pipeline.3rdLvlSummarySheets : plot.set.list.reports: no visible
binding for global variable ‘group.colors’
pipeline.3rdLvlSummarySheets : plot.set.list.reports: no visible
binding for global variable ‘indata’
pipeline.3rdLvlSummarySheets : plot.set.list.reports: no visible global
function definition for ‘abline’
pipeline.3rdLvlSummarySheets : plot.set.list.reports: no visible
binding for global variable ‘groupwise.group.colors’
pipeline.3rdLvlSummarySheets : plot.set.list.reports: no visible global
function definition for ‘boxplot’
pipeline.3rdLvlSummarySheets : plot.set.list.reports: no visible global
function definition for ‘legend’
pipeline.3rdLvlSummarySheets : plot.set.list.reports: no visible global
function definition for ‘stars’
pipeline.3rdLvlSummarySheets : plot.set.list.reports : <anonymous>: no
visible binding for global variable ‘group.labels’
pipeline.3rdLvlSummarySheets: no visible binding for global variable
‘files.name’
pipeline.3rdLvlSummarySheets: no visible global function definition for
‘pdf’
pipeline.3rdLvlSummarySheets: no visible binding for global variable
‘spot.list.overexpression’
pipeline.3rdLvlSummarySheets: no visible global function definition for
‘dev.off’
pipeline.3rdLvlSummarySheets: no visible binding for global variable
‘spot.list.underexpression’
pipeline.3rdLvlSummarySheets: no visible binding for global variable
‘spot.list.kmeans’
pipeline.3rdLvlSummarySheets: no visible binding for global variable
‘group.labels’
pipeline.3rdLvlSummarySheets: no visible binding for global variable
‘spot.list.group.overexpression’
pipeline.3rdLvlSummarySheets: no visible binding for global variable
‘spot.list.dmap’
pipeline.affymetrixQualityCheck: no visible binding for global variable
‘indata’
pipeline.affymetrixQualityCheck: no visible global function definition
for ‘par’
pipeline.affymetrixQualityCheck: no visible global function definition
for ‘barplot’
pipeline.affymetrixQualityCheck: no visible binding for global variable
‘group.colors’
pipeline.affymetrixQualityCheck: no visible global function definition
for ‘box’
pipeline.affymetrixQualityCheck: no visible binding for global variable
‘group.labels’
pipeline.affymetrixQualityCheck: no visible global function definition
for ‘boxplot’
pipeline.affymetrixQualityCheck: no visible binding for global variable
‘groupwise.group.colors’
pipeline.affymetrixQualityCheck: no visible global function definition
for ‘axis’
pipeline.affymetrixQualityCheck: no visible global function definition
for ‘abline’
pipeline.affymetrixQualityCheck: no visible global function definition
for ‘lines’
pipeline.calcStatistics: no visible binding for global variable
‘output.paths’
pipeline.calcStatistics: no visible binding for '<<-' assignment to
‘WAD.g.m’
pipeline.calcStatistics: no visible binding for global variable
‘indata’
pipeline.calcStatistics: no visible binding for global variable
‘WAD.g.m’
pipeline.calcStatistics: no visible binding for '<<-' assignment to
‘t.g.m’
pipeline.calcStatistics: no visible binding for '<<-' assignment to
‘p.g.m’
pipeline.calcStatistics: no visible binding for '<<-' assignment to
‘n.0.m’
pipeline.calcStatistics: no visible binding for global variable ‘n.0.m’
pipeline.calcStatistics: no visible binding for '<<-' assignment to
‘perc.DE.m’
pipeline.calcStatistics: no visible binding for global variable
‘perc.DE.m’
pipeline.calcStatistics: no visible binding for '<<-' assignment to
‘fdr.g.m’
pipeline.calcStatistics: no visible binding for '<<-' assignment to
‘Fdr.g.m’
pipeline.calcStatistics: no visible binding for global variable
‘indata.gene.mean’
pipeline.calcStatistics: no visible binding for global variable ‘sd’
pipeline.calcStatistics: no visible binding for global variable ‘t.g.m’
pipeline.calcStatistics: no visible binding for global variable ‘p.g.m’
pipeline.calcStatistics: no visible binding for global variable
‘fdr.g.m’
pipeline.calcStatistics: no visible binding for global variable
‘Fdr.g.m’
pipeline.calcStatistics: no visible global function definition for
‘bmp’
pipeline.calcStatistics: no visible global function definition for
‘par’
pipeline.calcStatistics: no visible global function definition for
‘mtext’
pipeline.calcStatistics: no visible global function definition for
‘points’
pipeline.calcStatistics: no visible global function definition for
‘legend’
pipeline.calcStatistics: no visible global function definition for
‘dev.off’
pipeline.calcStatistics: no visible binding for '<<-' assignment to
‘t.m’
pipeline.calcStatistics: no visible binding for '<<-' assignment to
‘p.m’
pipeline.calcStatistics: no visible binding for global variable
‘preferences’
pipeline.calcStatistics: no visible binding for global variable
‘som.nodes’
pipeline.calcStatistics: no visible binding for global variable ‘t.m’
pipeline.calcStatistics: no visible global function definition for
‘na.omit’
pipeline.calcStatistics: no visible binding for global variable ‘p.m’
pipeline.cancerHallmarks : <anonymous>: no visible binding for global
variable ‘gs.def.list’
pipeline.cancerHallmarks : <anonymous>: no visible binding for global
variable ‘gene.ids’
pipeline.cancerHallmarks: no visible binding for global variable
‘indata’
pipeline.cancerHallmarks : <anonymous>: no visible binding for global
variable ‘unique.protein.ids’
pipeline.cancerHallmarks : <anonymous>: no visible binding for global
variable ‘t.ensID.m’
pipeline.cancerHallmarks: no visible binding for global variable
‘preferences’
pipeline.cancerHallmarks : <anonymous>: no visible global function
definition for ‘na.omit’
pipeline.cancerHallmarks: no visible binding for global variable
‘files.name’
pipeline.cancerHallmarks: no visible global function definition for
‘pdf’
pipeline.cancerHallmarks: no visible global function definition for
‘layout’
pipeline.cancerHallmarks: no visible binding for global variable
‘group.labels’
pipeline.cancerHallmarks: no visible global function definition for
‘par’
pipeline.cancerHallmarks: no visible global function definition for
‘boxplot’
pipeline.cancerHallmarks: no visible binding for global variable
‘groupwise.group.colors’
pipeline.cancerHallmarks: no visible global function definition for
‘abline’
pipeline.cancerHallmarks: no visible binding for global variable
‘som.nodes’
pipeline.cancerHallmarks: no visible global function definition for
‘color.palette.heatmaps’
pipeline.cancerHallmarks: no visible global function definition for
‘na.omit’
pipeline.cancerHallmarks: no visible global function definition for
‘title’
pipeline.cancerHallmarks: no visible global function definition for
‘box’
pipeline.cancerHallmarks: no visible global function definition for
‘frame’
pipeline.cancerHallmarks: no visible global function definition for
‘legend’
pipeline.cancerHallmarks: no visible global function definition for
‘dev.off’
pipeline.chromosomeExpressionReports: no visible binding for global
variable ‘metadata’
pipeline.chromosomeExpressionReports: no visible binding for global
variable ‘gene.positions.list’
pipeline.chromosomeExpressionReports : <anonymous>: no visible binding
for global variable ‘gene.ids’
pipeline.chromosomeExpressionReports: no visible binding for global
variable ‘indata’
pipeline.chromosomeExpressionReports : <anonymous>: no visible binding
for global variable ‘unique.protein.ids’
pipeline.chromosomeExpressionReports : <anonymous>: no visible binding
for global variable ‘t.ensID.m’
pipeline.chromosomeExpressionReports: no visible binding for global
variable ‘files.name’
pipeline.chromosomeExpressionReports: no visible global function
definition for ‘pdf’
pipeline.chromosomeExpressionReports: no visible global function
definition for ‘color.palette.heatmaps’
pipeline.chromosomeExpressionReports: no visible binding for global
variable ‘group.colors’
pipeline.chromosomeExpressionReports: no visible global function
definition for ‘par’
pipeline.chromosomeExpressionReports: no visible global function
definition for ‘image’
pipeline.chromosomeExpressionReports: no visible global function
definition for ‘box’
pipeline.chromosomeExpressionReports: no visible global function
definition for ‘axis’
pipeline.chromosomeExpressionReports: no visible global function
definition for ‘title’
pipeline.chromosomeExpressionReports: no visible global function
definition for ‘dev.off’
pipeline.detectEnsemblDataset: no visible binding for '<<-' assignment
to ‘preferences’
pipeline.detectEnsemblDataset: no visible binding for global variable
‘preferences’
pipeline.detectEnsemblDataset: no visible binding for global variable
‘indata’
pipeline.detectSpotsIntegral: no visible binding for global variable
‘metadata’
pipeline.detectSpotsIntegral: no visible binding for global variable
‘indata’
pipeline.detectSpotsIntegral: no visible binding for global variable
‘preferences’
pipeline.detectSpotsIntegral: no visible binding for '<<-' assignment
to ‘spot.list.overexpression’
pipeline.detectSpotsIntegral: no visible binding for global variable
‘spot.list.overexpression’
pipeline.detectSpotsIntegral: no visible binding for global variable
‘som.nodes’
pipeline.detectSpotsIntegral: no visible binding for global variable
‘som.result’
pipeline.detectSpotsIntegral : <anonymous>: no visible binding for
global variable ‘metadata’
pipeline.detectSpotsIntegral : <anonymous>: no visible binding for
global variable ‘indata’
pipeline.detectSpotsIntegral: no visible binding for '<<-' assignment
to ‘spot.list.underexpression’
pipeline.detectSpotsIntegral: no visible binding for global variable
‘spot.list.underexpression’
pipeline.detectSpotsIntegral: no visible binding for '<<-' assignment
to ‘spot.list.correlation’
pipeline.detectSpotsIntegral: no visible binding for global variable
‘spot.list.correlation’
pipeline.detectSpotsIntegral: no visible global function definition for
‘cor’
pipeline.detectSpotsIntegral: no visible global function definition for
‘kmeans’
pipeline.detectSpotsIntegral: no visible binding for '<<-' assignment
to ‘spot.list.kmeans’
pipeline.detectSpotsIntegral: no visible binding for global variable
‘spot.list.kmeans’
pipeline.detectSpotsIntegral: no visible binding for global variable
‘group.labels’
pipeline.detectSpotsIntegral: no visible binding for '<<-' assignment
to ‘spot.list.group.overexpression’
pipeline.detectSpotsIntegral: no visible binding for global variable
‘spot.list.group.overexpression’
pipeline.detectSpotsIntegral : <anonymous>: no visible binding for
global variable ‘preferences’
pipeline.detectSpotsIntegral : <anonymous>: no visible global function
definition for ‘dist’
pipeline.detectSpotsIntegral: no visible binding for '<<-' assignment
to ‘spot.list.dmap’
pipeline.detectSpotsIntegral: no visible binding for global variable
‘spot.list.dmap’
pipeline.detectSpotsIntegral: no visible global function definition for
‘na.omit’
pipeline.detectSpotsIntegral : <anonymous>: no visible global function
definition for ‘sd’
pipeline.detectSpotsIntegral : <anonymous>: no visible binding for
global variable ‘spot.list.dmap’
pipeline.detectSpotsSamples: no visible binding for '<<-' assignment to
‘spot.list.samples’
pipeline.detectSpotsSamples: no visible binding for global variable
‘indata’
pipeline.detectSpotsSamples: no visible binding for global variable
‘spot.list.samples’
pipeline.differenceAnalyses: no visible binding for global variable
‘group.labels’
pipeline.differenceAnalyses: no visible global function definition for
‘combn’
pipeline.differenceAnalyses : <anonymous>: no visible binding for
global variable ‘group.labels’
pipeline.differenceAnalyses: no visible binding for global variable
‘files.name’
pipeline.differenceAnalyses: no visible binding for '<<-' assignment to
‘WAD.g.m’
pipeline.differenceAnalyses: no visible binding for global variable
‘indata’
pipeline.differenceAnalyses: no visible binding for '<<-' assignment to
‘t.g.m’
pipeline.differenceAnalyses: no visible binding for '<<-' assignment to
‘p.g.m’
pipeline.differenceAnalyses: no visible binding for '<<-' assignment to
‘fdr.g.m’
pipeline.differenceAnalyses: no visible binding for '<<-' assignment to
‘Fdr.g.m’
pipeline.differenceAnalyses: no visible binding for '<<-' assignment to
‘n.0.m’
pipeline.differenceAnalyses: no visible binding for global variable
‘n.0.m’
pipeline.differenceAnalyses: no visible binding for '<<-' assignment to
‘perc.DE.m’
pipeline.differenceAnalyses: no visible binding for global variable
‘perc.DE.m’
pipeline.differenceAnalyses: no visible binding for global variable
‘metadata’
pipeline.differenceAnalyses: no visible binding for global variable
‘var’
pipeline.differenceAnalyses: no visible binding for global variable
‘t.g.m’
pipeline.differenceAnalyses: no visible binding for global variable
‘p.g.m’
pipeline.differenceAnalyses: no visible global function definition for
‘pt’
pipeline.differenceAnalyses: no visible binding for global variable
‘fdr.g.m’
pipeline.differenceAnalyses: no visible binding for global variable
‘Fdr.g.m’
pipeline.differenceAnalyses: no visible binding for global variable
‘WAD.g.m’
pipeline.differenceAnalyses: no visible binding for '<<-' assignment to
‘indata’
pipeline.differenceAnalyses: no visible binding for '<<-' assignment to
‘metadata’
pipeline.differenceAnalyses: no visible binding for '<<-' assignment to
‘group.labels’
pipeline.differenceAnalyses: no visible binding for '<<-' assignment to
‘group.colors’
pipeline.differenceAnalyses: no visible binding for global variable
‘group.colors’
pipeline.differenceAnalyses: no visible binding for '<<-' assignment to
‘output.paths’
pipeline.entropyProfiles: no visible binding for global variable
‘files.name’
pipeline.entropyProfiles: no visible global function definition for
‘pdf’
pipeline.entropyProfiles: no visible global function definition for
‘par’
pipeline.entropyProfiles: no visible global function definition for
‘barplot’
pipeline.entropyProfiles: no visible binding for global variable
‘metadata’
pipeline.entropyProfiles: no visible binding for global variable
‘group.colors’
pipeline.entropyProfiles: no visible binding for global variable
‘indata’
pipeline.entropyProfiles: no visible global function definition for
‘box’
pipeline.entropyProfiles: no visible binding for global variable
‘group.labels’
pipeline.entropyProfiles: no visible global function definition for
‘boxplot’
pipeline.entropyProfiles: no visible binding for global variable
‘groupwise.group.colors’
pipeline.entropyProfiles: no visible global function definition for
‘axis’
pipeline.entropyProfiles: no visible binding for global variable ‘var’
pipeline.entropyProfiles: no visible global function definition for
‘quantile’
pipeline.entropyProfiles : <anonymous>: no visible global function
definition for ‘hist’
pipeline.entropyProfiles : <anonymous>: no visible binding for global
variable ‘preferences’
pipeline.entropyProfiles: no visible binding for global variable
‘som.result’
pipeline.entropyProfiles: no visible global function definition for
‘dev.off’
pipeline.geneLists: no visible binding for global variable
‘output.paths’
pipeline.geneLists: no visible binding for global variable ‘indata’
pipeline.geneLists: no visible binding for global variable ‘p.g.m’
pipeline.geneLists: no visible binding for global variable ‘gene.names’
pipeline.geneLists: no visible binding for global variable ‘files.name’
pipeline.geneLists: no visible binding for global variable
‘gs.def.list’
pipeline.geneLists: no visible binding for global variable ‘WAD.g.m’
pipeline.geneLists: no visible binding for global variable ‘t.g.m’
pipeline.geneLists: no visible binding for global variable ‘fdr.g.m’
pipeline.geneLists: no visible binding for global variable ‘Fdr.g.m’
pipeline.geneLists: no visible binding for global variable
‘gene.coordinates’
pipeline.geneLists: no visible binding for global variable
‘gene.positions’
pipeline.geneLists: no visible binding for global variable
‘gene.descriptions’
pipeline.geneLists: no visible binding for global variable ‘perc.DE.m’
pipeline.geneLists: no visible global function definition for
‘write.csv2’
pipeline.geneLists: no visible binding for global variable
‘preferences’
pipeline.geneLists: no visible binding for global variable
‘spot.list.samples’
pipeline.genesetOverviews: no visible binding for global variable
‘files.name’
pipeline.genesetOverviews: no visible global function definition for
‘pdf’
pipeline.genesetOverviews: no visible binding for global variable
‘preferences’
pipeline.genesetOverviews : <anonymous>: no visible binding for global
variable ‘gs.def.list’
pipeline.genesetOverviews: no visible binding for global variable
‘gs.def.list’
pipeline.genesetOverviews: no visible binding for global variable
‘samples.GSZ.scores’
pipeline.genesetOverviews: no visible binding for global variable
‘indata’
pipeline.genesetOverviews: no visible global function definition for
‘quantile’
pipeline.genesetOverviews: no visible global function definition for
‘color.palette.heatmaps’
pipeline.genesetOverviews: no visible binding for global variable
‘group.colors’
pipeline.genesetOverviews: no visible global function definition for
‘par’
pipeline.genesetOverviews: no visible global function definition for
‘image’
pipeline.genesetOverviews: no visible global function definition for
‘box’
pipeline.genesetOverviews: no visible global function definition for
‘axis’
pipeline.genesetOverviews: no visible global function definition for
‘mtext’
pipeline.genesetOverviews: no visible binding for global variable
‘group.labels’
pipeline.genesetOverviews : <anonymous>: no visible binding for global
variable ‘group.labels’
pipeline.genesetOverviews : <anonymous>: no visible global function
definition for ‘hclust’
pipeline.genesetOverviews : <anonymous>: no visible global function
definition for ‘dist’
pipeline.genesetOverviews: no visible binding for global variable
‘spot.list.samples’
pipeline.genesetOverviews: no visible global function definition for
‘hist’
pipeline.genesetOverviews: no visible global function definition for
‘abline’
pipeline.genesetOverviews: no visible global function definition for
‘lines’
pipeline.genesetOverviews: no visible global function definition for
‘legend’
pipeline.genesetOverviews: no visible global function definition for
‘dev.off’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
‘samples.GSZ.scores’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
‘files.name’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘quantile’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘sd’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
‘gs.def.list’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘pdf’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘layout’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
‘indata’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
‘gene.ids’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
‘sd’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
‘gene.names’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘hclust’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘dist’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘par’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘barplot’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
‘group.colors’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘abline’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘axis’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘mtext’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘frame’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘legend’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
‘groupwise.group.colors’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘image’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘box’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘color.palette.heatmaps’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
‘preferences’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
‘som.nodes’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘na.omit’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘title’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
‘group.labels’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘boxplot’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘dev.off’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
‘gene.coordinates’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
‘gene.descriptions’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘write.csv2’
pipeline.genesetStatisticIntegral : spot.fisher.p: no visible global
function definition for ‘na.omit’
pipeline.genesetStatisticIntegral : spot.fisher.p: no visible binding
for global variable ‘gene.ids’
pipeline.genesetStatisticIntegral : spot.fisher.p: no visible binding
for global variable ‘unique.protein.ids’
pipeline.genesetStatisticIntegral : spot.fisher.p: no visible binding
for global variable ‘gs.def.list’
pipeline.genesetStatisticIntegral: no visible binding for '<<-'
assignment to ‘spot.list.overexpression’
pipeline.genesetStatisticIntegral: no visible binding for global
variable ‘spot.list.overexpression’
pipeline.genesetStatisticIntegral: no visible binding for '<<-'
assignment to ‘spot.list.underexpression’
pipeline.genesetStatisticIntegral: no visible binding for global
variable ‘spot.list.underexpression’
pipeline.genesetStatisticIntegral: no visible binding for global
variable ‘spot.list.correlation’
pipeline.genesetStatisticIntegral: no visible binding for '<<-'
assignment to ‘spot.list.correlation’
pipeline.genesetStatisticIntegral: no visible binding for '<<-'
assignment to ‘spot.list.kmeans’
pipeline.genesetStatisticIntegral: no visible binding for global
variable ‘spot.list.kmeans’
pipeline.genesetStatisticIntegral: no visible binding for global
variable ‘group.labels’
pipeline.genesetStatisticIntegral: no visible binding for '<<-'
assignment to ‘spot.list.group.overexpression’
pipeline.genesetStatisticIntegral: no visible binding for global
variable ‘spot.list.group.overexpression’
pipeline.genesetStatisticIntegral: no visible binding for '<<-'
assignment to ‘spot.list.dmap’
pipeline.genesetStatisticIntegral: no visible binding for global
variable ‘spot.list.dmap’
pipeline.genesetStatisticSamples: no visible binding for global
variable ‘indata’
pipeline.genesetStatisticSamples: no visible binding for '<<-'
assignment to ‘t.ensID.m’
pipeline.genesetStatisticSamples: no visible binding for global
variable ‘t.g.m’
pipeline.genesetStatisticSamples: no visible binding for global
variable ‘gene.ids’
pipeline.genesetStatisticSamples: no visible binding for global
variable ‘t.ensID.m’
pipeline.genesetStatisticSamples: no visible binding for global
variable ‘preferences’
pipeline.genesetStatisticSamples: no visible binding for global
variable ‘gs.def.list’
pipeline.genesetStatisticSamples: no visible binding for global
variable ‘unique.protein.ids’
pipeline.genesetStatisticSamples : <anonymous>: no visible binding for
global variable ‘t.ensID.m’
pipeline.genesetStatisticSamples : <anonymous>: no visible binding for
global variable ‘unique.protein.ids’
pipeline.genesetStatisticSamples: no visible global function definition
for ‘ecdf’
pipeline.genesetStatisticSamples: no visible binding for '<<-'
assignment to ‘spot.list.samples’
pipeline.genesetStatisticSamples: no visible binding for global
variable ‘spot.list.samples’
pipeline.genesetStatisticSamples : <anonymous>: no visible binding for
global variable ‘spot.list.samples’
pipeline.genesetStatisticSamples : <anonymous>: no visible binding for
global variable ‘gs.def.list’
pipeline.genesetStatisticSamples : <anonymous>: no visible binding for
global variable ‘preferences’
pipeline.genesetStatisticSamples: no visible binding for '<<-'
assignment to ‘samples.GSZ.scores’
pipeline.genesetStatisticSamples: no visible binding for global
variable ‘output.paths’
pipeline.genesetStatisticSamples: no visible global function definition
for ‘write.csv2’
pipeline.genesetStatisticSamples: no visible binding for global
variable ‘samples.GSZ.scores’
pipeline.groupAnalysis: no visible binding for global variable
‘group.labels’
pipeline.groupAnalysis: no visible binding for global variable
‘files.name’
pipeline.groupAnalysis: no visible binding for '<<-' assignment to
‘WAD.g.m’
pipeline.groupAnalysis: no visible binding for global variable ‘indata’
pipeline.groupAnalysis: no visible binding for '<<-' assignment to
‘t.g.m’
pipeline.groupAnalysis: no visible binding for '<<-' assignment to
‘p.g.m’
pipeline.groupAnalysis: no visible binding for '<<-' assignment to
‘fdr.g.m’
pipeline.groupAnalysis: no visible binding for '<<-' assignment to
‘Fdr.g.m’
pipeline.groupAnalysis: no visible binding for '<<-' assignment to
‘n.0.m’
pipeline.groupAnalysis: no visible binding for global variable ‘n.0.m’
pipeline.groupAnalysis: no visible binding for '<<-' assignment to
‘perc.DE.m’
pipeline.groupAnalysis: no visible binding for global variable
‘perc.DE.m’
pipeline.groupAnalysis: no visible binding for global variable ‘t.g.m’
pipeline.groupAnalysis : <anonymous>: no visible global function
definition for ‘sd’
pipeline.groupAnalysis: no visible binding for global variable ‘p.g.m’
pipeline.groupAnalysis: no visible global function definition for ‘pt’
pipeline.groupAnalysis: no visible binding for global variable
‘fdr.g.m’
pipeline.groupAnalysis: no visible binding for global variable
‘Fdr.g.m’
pipeline.groupAnalysis: no visible binding for global variable
‘WAD.g.m’
pipeline.groupAnalysis: no visible binding for '<<-' assignment to
‘metadata’
pipeline.groupAnalysis: no visible binding for global variable
‘metadata’
pipeline.groupAnalysis: no visible binding for '<<-' assignment to
‘indata’
pipeline.groupAnalysis: no visible binding for global variable
‘indata.gene.mean’
pipeline.groupAnalysis: no visible binding for '<<-' assignment to
‘indata.gene.mean’
pipeline.groupAnalysis: no visible binding for '<<-' assignment to
‘group.colors’
pipeline.groupAnalysis: no visible binding for global variable
‘group.colors’
pipeline.groupAnalysis: no visible binding for '<<-' assignment to
‘group.labels’
pipeline.groupAnalysis: no visible binding for '<<-' assignment to
‘output.paths’
pipeline.groupAssignment: no visible binding for global variable
‘group.labels’
pipeline.groupAssignment: no visible binding for global variable
‘files.name’
pipeline.groupAssignment: no visible binding for global variable
‘preferences’
pipeline.groupAssignment: no visible binding for global variable
‘pat.labels’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
‘opt.cluster.number’
pipeline.groupAssignment: no visible binding for global variable
‘opt.cluster.number’
pipeline.groupAssignment: no visible binding for global variable
‘indata’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
‘group.labels’
pipeline.groupAssignment: no visible global function definition for
‘pdf’
pipeline.groupAssignment: no visible global function definition for
‘barplot’
pipeline.groupAssignment: no visible global function definition for
‘box’
pipeline.groupAssignment: no visible global function definition for
‘lines’
pipeline.groupAssignment: no visible global function definition for
‘abline’
pipeline.groupAssignment: no visible global function definition for
‘dev.off’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
‘pat.labels’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
‘group.colors’
pipeline.groupAssignment: no visible binding for global variable
‘group.colors’
pipeline.groupAssignment: no visible global function definition for
‘colorRampPalette’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
‘groupwise.group.colors’
pipeline.groupAssignment: no visible binding for global variable
‘groupwise.group.colors’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
‘t.g.m’
pipeline.groupAssignment: no visible binding for global variable
‘t.g.m’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
‘p.g.m’
pipeline.groupAssignment: no visible binding for global variable
‘p.g.m’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
‘fdr.g.m’
pipeline.groupAssignment: no visible binding for global variable
‘fdr.g.m’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
‘Fdr.g.m’
pipeline.groupAssignment: no visible binding for global variable
‘Fdr.g.m’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
‘WAD.g.m’
pipeline.groupAssignment: no visible binding for global variable
‘WAD.g.m’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
‘n.0.m’
pipeline.groupAssignment: no visible binding for global variable
‘n.0.m’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
‘perc.DE.m’
pipeline.groupAssignment: no visible binding for global variable
‘perc.DE.m’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
‘t.m’
pipeline.groupAssignment: no visible binding for global variable ‘t.m’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
‘p.m’
pipeline.groupAssignment: no visible binding for global variable ‘p.m’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
‘indata’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
‘metadata’
pipeline.groupAssignment: no visible binding for global variable
‘metadata’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
‘indata.sample.mean’
pipeline.groupAssignment: no visible binding for global variable
‘indata.sample.mean’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
‘spot.list.samples’
pipeline.groupAssignment: no visible binding for global variable
‘spot.list.samples’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
‘group.silhouette.coef’
pipeline.groupAssignment: no visible global function definition for
‘cor’
pipeline.groupAssignment : <anonymous>: no visible binding for global
variable ‘group.labels’
pipeline.groupAssignment: no visible binding for global variable
‘group.silhouette.coef’
pipeline.groupSpecificGenesets: no visible global function definition
for ‘sd’
pipeline.groupSpecificGenesets: no visible binding for global variable
‘samples.GSZ.scores’
pipeline.groupSpecificGenesets: no visible binding for global variable
‘group.labels’
pipeline.groupSpecificGenesets : <anonymous>: no visible global
function definition for ‘wilcox.test’
pipeline.groupSpecificGenesets : <anonymous>: no visible binding for
global variable ‘group.labels’
pipeline.groupSpecificGenesets: no visible global function definition
for ‘pdf’
pipeline.groupSpecificGenesets: no visible binding for global variable
‘files.name’
pipeline.groupSpecificGenesets: no visible global function definition
for ‘layout’
pipeline.groupSpecificGenesets: no visible global function definition
for ‘par’
pipeline.groupSpecificGenesets: no visible global function definition
for ‘barplot’
pipeline.groupSpecificGenesets: no visible binding for global variable
‘group.colors’
pipeline.groupSpecificGenesets: no visible binding for global variable
‘indata’
pipeline.groupSpecificGenesets: no visible global function definition
for ‘abline’
pipeline.groupSpecificGenesets: no visible global function definition
for ‘title’
pipeline.groupSpecificGenesets: no visible global function definition
for ‘mtext’
pipeline.groupSpecificGenesets: no visible binding for global variable
‘preferences’
pipeline.groupSpecificGenesets: no visible binding for global variable
‘som.nodes’
pipeline.groupSpecificGenesets: no visible binding for global variable
‘gene.ids’
pipeline.groupSpecificGenesets: no visible binding for global variable
‘gs.def.list’
pipeline.groupSpecificGenesets: no visible global function definition
for ‘na.omit’
pipeline.groupSpecificGenesets: no visible global function definition
for ‘color.palette.heatmaps’
pipeline.groupSpecificGenesets: no visible global function definition
for ‘box’
pipeline.groupSpecificGenesets: no visible global function definition
for ‘dev.off’
pipeline.groupSpecificGenesets: no visible global function definition
for ‘write.csv2’
pipeline.groupSpecificGenesets : <anonymous>: no visible global
function definition for ‘aov’
pipeline.groupSpecificGenesets: no visible global function definition
for ‘text’
pipeline.groupSpecificGenesets: no visible binding for global variable
‘groupwise.group.colors’
pipeline.htmlDifferencesSummary: no visible binding for global variable
‘files.name’
pipeline.htmlDifferencesSummary: no visible binding for global variable
‘indata’
pipeline.htmlGenesetAnalysis: no visible binding for global variable
‘preferences’
pipeline.htmlGenesetAnalysis: no visible binding for global variable
‘files.name’
pipeline.htmlGenesetAnalysis: no visible binding for global variable
‘gs.def.list’
pipeline.htmlGroupSummary: no visible binding for global variable
‘group.labels’
pipeline.htmlGroupSummary: no visible binding for global variable
‘files.name’
pipeline.htmlGroupSummary: no visible binding for global variable
‘preferences’
pipeline.htmlGroupSummary: no visible binding for global variable
‘indata’
pipeline.htmlIntegralSummary: no visible binding for global variable
‘files.name’
pipeline.htmlIntegralSummary: no visible binding for global variable
‘spot.list.overexpression’
pipeline.htmlIntegralSummary: no visible binding for global variable
‘group.labels’
pipeline.htmlIntegralSummary: no visible binding for global variable
‘spot.list.group.overexpression’
pipeline.htmlIntegralSummary: no visible binding for global variable
‘spot.list.underexpression’
pipeline.htmlIntegralSummary: no visible binding for global variable
‘spot.list.correlation’
pipeline.htmlIntegralSummary: no visible binding for global variable
‘spot.list.kmeans’
pipeline.htmlIntegralSummary: no visible binding for global variable
‘spot.list.dmap’
pipeline.htmlSampleSummary: no visible binding for global variable
‘files.name’
pipeline.htmlSampleSummary: no visible binding for global variable
‘group.labels’
pipeline.htmlSampleSummary: no visible binding for global variable
‘indata’
pipeline.htmlSummary: no visible binding for global variable
‘files.name’
pipeline.htmlSummary: no visible binding for global variable ‘indata’
pipeline.htmlSummary: no visible binding for global variable
‘group.labels’
pipeline.htmlSummary: no visible binding for global variable
‘preferences’
pipeline.patAssignment: no visible binding for global variable
‘preferences’
pipeline.patAssignment: no visible global function definition for ‘sd’
pipeline.patAssignment: no visible binding for '<<-' assignment to
‘pat.labels’
pipeline.patAssignment: no visible binding for global variable
‘pat.labels’
pipeline.prepare: no visible binding for global variable ‘preferences’
pipeline.prepare: no visible binding for '<<-' assignment to
‘preferences’
pipeline.prepare : <anonymous>: no visible binding for global variable
‘indata’
pipeline.prepare : <anonymous> : <anonymous>: no visible global
function definition for ‘na.omit’
pipeline.prepare: no visible binding for global variable ‘indata’
pipeline.prepare: no visible binding for '<<-' assignment to
‘group.labels’
pipeline.prepare: no visible binding for '<<-' assignment to
‘group.colors’
pipeline.prepare: no visible binding for '<<-' assignment to ‘indata’
pipeline.prepare: no visible binding for global variable ‘group.labels’
pipeline.prepare: no visible binding for global variable ‘group.colors’
pipeline.prepare: no visible binding for '<<-' assignment to
‘files.name’
pipeline.prepare: no visible binding for global variable ‘files.name’
pipeline.prepare: no visible binding for '<<-' assignment to
‘output.paths’
pipeline.prepare: no visible binding for global variable
‘color.palette.portraits’
pipeline.prepare: no visible binding for '<<-' assignment to
‘color.palette.portraits’
pipeline.prepare: no visible global function definition for
‘colorRampPalette’
pipeline.prepare: no visible binding for global variable
‘color.palette.heatmaps’
pipeline.prepare: no visible binding for '<<-' assignment to
‘color.palette.heatmaps’
pipeline.prepare: no visible global function definition for ‘col2rgb’
pipeline.prepare : <anonymous>: no visible global function definition
for ‘rgb’
pipeline.prepare: no visible binding for '<<-' assignment to
‘groupwise.group.colors’
pipeline.prepare: no visible binding for global variable
‘groupwise.group.colors’
pipeline.prepare: no visible binding for '<<-' assignment to
‘indata.sample.mean’
pipeline.prepare: no visible binding for '<<-' assignment to
‘indata.gene.mean’
pipeline.prepare: no visible binding for global variable
‘indata.gene.mean’
pipeline.prepare: no visible binding for '<<-' assignment to
‘som.result’
pipeline.prepare: no visible binding for global variable ‘som.result’
pipeline.prepare: no visible binding for '<<-' assignment to ‘metadata’
pipeline.prepare: no visible binding for global variable ‘metadata’
pipeline.prepare: no visible binding for '<<-' assignment to
‘gene.coordinates’
pipeline.prepare: no visible binding for global variable
‘gene.coordinates’
pipeline.prepare: no visible binding for '<<-' assignment to
‘som.nodes’
pipeline.prepare: no visible binding for global variable ‘som.nodes’
pipeline.prepare: no visible binding for global variable ‘gene.names’
pipeline.prepare: no visible binding for global variable
‘gene.positions’
pipeline.prepare: no visible binding for global variable
‘gene.descriptions’
pipeline.prepare: no visible global function definition for
‘write.csv2’
pipeline.prepareAnnotation: no visible binding for '<<-' assignment to
‘gene.ids’
pipeline.prepareAnnotation: no visible binding for global variable
‘indata’
pipeline.prepareAnnotation: no visible binding for global variable
‘gene.ids’
pipeline.prepareAnnotation: no visible binding for '<<-' assignment to
‘gene.names’
pipeline.prepareAnnotation: no visible binding for global variable
‘gene.names’
pipeline.prepareAnnotation: no visible binding for '<<-' assignment to
‘gene.descriptions’
pipeline.prepareAnnotation: no visible binding for global variable
‘gene.descriptions’
pipeline.prepareAnnotation: no visible binding for '<<-' assignment to
‘gene.positions’
pipeline.prepareAnnotation: no visible binding for global variable
‘gene.positions’
pipeline.prepareAnnotation: no visible binding for '<<-' assignment to
‘gene.positions.table’
pipeline.prepareAnnotation: no visible binding for '<<-' assignment to
‘gene.positions.list’
pipeline.prepareAnnotation: no visible binding for '<<-' assignment to
‘preferences’
pipeline.prepareAnnotation: no visible binding for global variable
‘preferences’
pipeline.prepareAnnotation: no visible binding for global variable
‘gene.positions.table’
pipeline.prepareAnnotation: no visible binding for global variable
‘gene.positions.list’
pipeline.prepareAnnotation : <anonymous>: no visible binding for global
variable ‘gene.positions.table’
pipeline.prepareAnnotation: no visible binding for '<<-' assignment to
‘unique.protein.ids’
pipeline.prepareAnnotation: no visible binding for global variable
‘unique.protein.ids’
pipeline.prepareAnnotation: no visible binding for '<<-' assignment to
‘gs.def.list’
pipeline.prepareAnnotation: no visible binding for global variable
‘gs.def.list’
pipeline.prepareAnnotation: no visible binding for global variable
‘head’
pipeline.prepareAnnotation : <anonymous>: no visible binding for global
variable ‘gene.ids’
pipeline.prepareAnnotation: no visible global function definition for
‘data’
pipeline.prepareAnnotation: no visible binding for global variable
‘opossom.genesets’
pipeline.prepareAnnotation : <anonymous>: no visible binding for global
variable ‘unique.protein.ids’
pipeline.qualityCheck: no visible binding for global variable
‘output.paths’
pipeline.qualityCheck : plot.poly.density: no visible binding for
global variable ‘indata’
pipeline.qualityCheck : plot.poly.density: no visible global function
definition for ‘par’
pipeline.qualityCheck : plot.poly.density: no visible global function
definition for ‘lines’
pipeline.qualityCheck : plot.poly.density: no visible global function
definition for ‘polygon’
pipeline.qualityCheck : plot.poly.density: no visible binding for
global variable ‘sd’
pipeline.qualityCheck: no visible binding for global variable ‘indata’
pipeline.qualityCheck : <anonymous>: no visible global function
definition for ‘density’
pipeline.qualityCheck: no visible global function definition for ‘pdf’
pipeline.qualityCheck: no visible global function definition for ‘par’
pipeline.qualityCheck: no visible binding for global variable ‘lines’
pipeline.qualityCheck: no visible binding for global variable
‘group.labels’
pipeline.qualityCheck: no visible binding for global variable
‘groupwise.group.colors’
pipeline.qualityCheck: no visible binding for global variable ‘sd’
pipeline.qualityCheck: no visible global function definition for
‘quantile’
pipeline.qualityCheck: no visible binding for global variable
‘indata.sample.mean’
pipeline.qualityCheck: no visible binding for global variable
‘group.colors’
pipeline.qualityCheck: no visible global function definition for
‘abline’
pipeline.qualityCheck: no visible global function definition for
‘legend’
pipeline.qualityCheck: no visible global function definition for ‘text’
pipeline.qualityCheck: no visible global function definition for
‘barplot’
pipeline.qualityCheck: no visible global function definition for ‘box’
pipeline.qualityCheck: no visible global function definition for
‘boxplot’
pipeline.qualityCheck: no visible global function definition for ‘axis’
pipeline.qualityCheck: no visible global function definition for
‘dev.off’
pipeline.sampleExpressionPortraits: no visible binding for global
variable ‘files.name’
pipeline.sampleExpressionPortraits: no visible global function
definition for ‘pdf’
pipeline.sampleExpressionPortraits: no visible global function
definition for ‘par’
pipeline.sampleExpressionPortraits: no visible binding for global
variable ‘group.labels’
pipeline.sampleExpressionPortraits: no visible global function
definition for ‘mtext’
pipeline.sampleExpressionPortraits: no visible binding for global
variable ‘groupwise.group.colors’
pipeline.sampleExpressionPortraits: no visible global function
definition for ‘image’
pipeline.sampleExpressionPortraits: no visible binding for global
variable ‘metadata’
pipeline.sampleExpressionPortraits: no visible binding for global
variable ‘preferences’
pipeline.sampleExpressionPortraits: no visible global function
definition for ‘color.palette.portraits’
pipeline.sampleExpressionPortraits: no visible global function
definition for ‘title’
pipeline.sampleExpressionPortraits: no visible binding for global
variable ‘indata’
pipeline.sampleExpressionPortraits: no visible binding for global
variable ‘group.silhouette.coef’
pipeline.sampleExpressionPortraits: no visible global function
definition for ‘box’
pipeline.sampleExpressionPortraits: no visible global function
definition for ‘persp’
pipeline.sampleExpressionPortraits: no visible global function
definition for ‘dev.off’
pipeline.sampleExpressionPortraits: no visible global function
definition for ‘text’
pipeline.sampleRankMaps: no visible binding for global variable
‘files.name’
pipeline.sampleRankMaps: no visible global function definition for
‘pdf’
pipeline.sampleRankMaps: no visible global function definition for
‘par’
pipeline.sampleRankMaps: no visible global function definition for
‘text’
pipeline.sampleRankMaps: no visible binding for global variable
‘group.labels’
pipeline.sampleRankMaps: no visible global function definition for
‘mtext’
pipeline.sampleRankMaps: no visible binding for global variable
‘groupwise.group.colors’
pipeline.sampleRankMaps: no visible binding for global variable
‘indata’
pipeline.sampleRankMaps: no visible binding for global variable
‘som.nodes’
pipeline.sampleRankMaps: no visible binding for global variable
‘preferences’
pipeline.sampleRankMaps: no visible global function definition for
‘image’
pipeline.sampleRankMaps: no visible global function definition for
‘color.palette.portraits’
pipeline.sampleRankMaps: no visible global function definition for
‘title’
pipeline.sampleRankMaps: no visible global function definition for
‘box’
pipeline.sampleRankMaps: no visible binding for global variable
‘WAD.g.m’
pipeline.sampleRankMaps: no visible binding for global variable ‘t.g.m’
pipeline.sampleRankMaps: no visible global function definition for
‘dev.off’
pipeline.summarySheetsGroups: no visible binding for global variable
‘metadata’
pipeline.summarySheetsGroups: no visible binding for global variable
‘group.labels’
pipeline.summarySheetsGroups : <anonymous>: no visible binding for
global variable ‘sd’
pipeline.summarySheetsGroups: no visible binding for global variable
‘files.name’
pipeline.summarySheetsGroups: no visible global function definition for
‘pdf’
pipeline.summarySheetsGroups: no visible global function definition for
‘par’
pipeline.summarySheetsGroups: no visible global function definition for
‘mtext’
pipeline.summarySheetsGroups: no visible binding for global variable
‘groupwise.group.colors’
pipeline.summarySheetsGroups: no visible global function definition for
‘image’
pipeline.summarySheetsGroups: no visible binding for global variable
‘preferences’
pipeline.summarySheetsGroups: no visible global function definition for
‘color.palette.portraits’
pipeline.summarySheetsGroups: no visible global function definition for
‘title’
pipeline.summarySheetsGroups: no visible global function definition for
‘box’
pipeline.summarySheetsGroups: no visible global function definition for
‘layout’
pipeline.summarySheetsGroups: no visible global function definition for
‘text’
pipeline.summarySheetsGroups: no visible global function definition for
‘colorRampPalette’
pipeline.summarySheetsGroups: no visible global function definition for
‘axis’
pipeline.summarySheetsGroups: no visible global function definition for
‘ecdf’
pipeline.summarySheetsGroups: no visible global function definition for
‘dev.off’
pipeline.summarySheetsGroups: no visible binding for global variable
‘group.silhouette.coef’
pipeline.summarySheetsGroups: no visible global function definition for
‘cor’
pipeline.summarySheetsGroups : <anonymous>: no visible binding for
global variable ‘group.labels’
pipeline.summarySheetsGroups: no visible binding for global variable
‘indata’
pipeline.summarySheetsGroups: no visible global function definition for
‘barplot’
pipeline.summarySheetsGroups: no visible binding for global variable
‘group.colors’
pipeline.summarySheetsGroups: no visible global function definition for
‘abline’
pipeline.summarySheetsGroups: no visible global function definition for
‘points’
pipeline.summarySheetsGroups: no visible global function definition for
‘boxplot’
pipeline.summarySheetsGroups : <anonymous>: no visible global function
definition for ‘axis’
pipeline.summarySheetsGroups : <anonymous>: no visible binding for
global variable ‘groupwise.group.colors’
pipeline.summarySheetsGroups: no visible global function definition for
‘hclust’
pipeline.summarySheetsGroups: no visible global function definition for
‘dist’
pipeline.summarySheetsGroups: no visible global function definition for
‘cutree’
pipeline.summarySheetsGroups: no visible global function definition for
‘quantile’
pipeline.summarySheetsGroups: no visible global function definition for
‘rect’
pipeline.summarySheetsIntegral : plot.set.list: no visible global
function definition for ‘pdf’
pipeline.summarySheetsIntegral : plot.set.list: no visible global
function definition for ‘layout’
pipeline.summarySheetsIntegral : plot.set.list: no visible global
function definition for ‘par’
pipeline.summarySheetsIntegral : plot.set.list: no visible global
function definition for ‘color.palette.portraits’
pipeline.summarySheetsIntegral : plot.set.list: no visible global
function definition for ‘colorRampPalette’
pipeline.summarySheetsIntegral : plot.set.list: no visible global
function definition for ‘image’
pipeline.summarySheetsIntegral : plot.set.list: no visible binding for
global variable ‘preferences’
pipeline.summarySheetsIntegral : plot.set.list: no visible global
function definition for ‘mtext’
pipeline.summarySheetsIntegral : plot.set.list: no visible global
function definition for ‘box’
pipeline.summarySheetsIntegral : plot.set.list: no visible global
function definition for ‘color.palette.heatmaps’
pipeline.summarySheetsIntegral : plot.set.list: no visible global
function definition for ‘axis’
pipeline.summarySheetsIntegral : plot.set.list: no visible global
function definition for ‘points’
pipeline.summarySheetsIntegral : plot.set.list: no visible global
function definition for ‘text’
pipeline.summarySheetsIntegral : plot.set.list : <anonymous>: no
visible global function definition for ‘head’
pipeline.summarySheetsIntegral : plot.set.list: no visible global
function definition for ‘legend’
pipeline.summarySheetsIntegral : plot.set.list: no visible binding for
global variable ‘indata’
pipeline.summarySheetsIntegral : plot.set.list: no visible binding for
global variable ‘group.labels’
pipeline.summarySheetsIntegral : plot.set.list: no visible binding for
global variable ‘group.colors’
pipeline.summarySheetsIntegral : plot.set.list: no visible global
function definition for ‘frame’
pipeline.summarySheetsIntegral : plot.set.list: no visible binding for
global variable ‘samples.GSZ.scores’
pipeline.summarySheetsIntegral : plot.set.list: no visible global
function definition for ‘sd’
pipeline.summarySheetsIntegral : plot.set.list: no visible global
function definition for ‘cor’
pipeline.summarySheetsIntegral : plot.set.list: no visible binding for
global variable ‘metadata’
pipeline.summarySheetsIntegral : plot.set.list: no visible global
function definition for ‘barplot’
pipeline.summarySheetsIntegral : plot.set.list : <anonymous>: no
visible binding for global variable ‘indata’
pipeline.summarySheetsIntegral : plot.set.list : <anonymous>: no
visible global function definition for ‘cor’
pipeline.summarySheetsIntegral : plot.set.list: no visible global
function definition for ‘rect’
pipeline.summarySheetsIntegral : plot.set.list: no visible binding for
global variable ‘gene.names’
pipeline.summarySheetsIntegral : plot.set.list: no visible binding for
global variable ‘gene.descriptions’
pipeline.summarySheetsIntegral : plot.set.list: no visible binding for
global variable ‘gs.def.list’
pipeline.summarySheetsIntegral : plot.set.list : <anonymous>: no
visible binding for global variable ‘gene.ids’
pipeline.summarySheetsIntegral : plot.set.list: no visible global
function definition for ‘hist’
pipeline.summarySheetsIntegral : plot.set.list: no visible global
function definition for ‘abline’
pipeline.summarySheetsIntegral : plot.set.list: no visible global
function definition for ‘lines’
pipeline.summarySheetsIntegral : plot.set.list: no visible global
function definition for ‘dev.off’
pipeline.summarySheetsIntegral : csv.set.list : <anonymous>: no visible
binding for global variable ‘indata’
pipeline.summarySheetsIntegral : csv.set.list : <anonymous>: no visible
global function definition for ‘cor’
pipeline.summarySheetsIntegral : csv.set.list: no visible binding for
global variable ‘indata’
pipeline.summarySheetsIntegral : csv.set.list: no visible global
function definition for ‘pt’
pipeline.summarySheetsIntegral : csv.set.list: no visible binding for
global variable ‘gene.names’
pipeline.summarySheetsIntegral : csv.set.list: no visible binding for
global variable ‘files.name’
pipeline.summarySheetsIntegral : csv.set.list: no visible binding for
global variable ‘gs.def.list’
pipeline.summarySheetsIntegral : csv.set.list: no visible binding for
global variable ‘indata.gene.mean’
pipeline.summarySheetsIntegral : csv.set.list: no visible binding for
global variable ‘sd’
pipeline.summarySheetsIntegral : csv.set.list: no visible binding for
global variable ‘gene.coordinates’
pipeline.summarySheetsIntegral : csv.set.list: no visible binding for
global variable ‘gene.positions’
pipeline.summarySheetsIntegral : csv.set.list: no visible binding for
global variable ‘gene.descriptions’
pipeline.summarySheetsIntegral : csv.set.list: no visible global
function definition for ‘write.csv2’
pipeline.summarySheetsIntegral: no visible binding for global variable
‘spot.list.overexpression’
pipeline.summarySheetsIntegral: no visible binding for global variable
‘spot.list.underexpression’
pipeline.summarySheetsIntegral: no visible binding for global variable
‘spot.list.correlation’
pipeline.summarySheetsIntegral: no visible binding for global variable
‘spot.list.kmeans’
pipeline.summarySheetsIntegral: no visible binding for global variable
‘spot.list.dmap’
pipeline.summarySheetsIntegral: no visible binding for global variable
‘group.labels’
pipeline.summarySheetsIntegral: no visible binding for global variable
‘spot.list.group.overexpression’
pipeline.summarySheetsIntegral: no visible binding for global variable
‘output.paths’
pipeline.summarySheetsPATs: no visible binding for global variable
‘files.name’
pipeline.summarySheetsPATs: no visible binding for global variable
‘metadata’
pipeline.summarySheetsPATs: no visible binding for global variable
‘pat.labels’
pipeline.summarySheetsPATs: no visible global function definition for
‘pdf’
pipeline.summarySheetsPATs: no visible global function definition for
‘hclust’
pipeline.summarySheetsPATs: no visible global function definition for
‘dist’
pipeline.summarySheetsPATs: no visible global function definition for
‘par’
pipeline.summarySheetsPATs: no visible global function definition for
‘frame’
pipeline.summarySheetsPATs: no visible binding for global variable
‘preferences’
pipeline.summarySheetsPATs: no visible global function definition for
‘color.palette.portraits’
pipeline.summarySheetsPATs: no visible global function definition for
‘layout’
pipeline.summarySheetsPATs: no visible global function definition for
‘text’
pipeline.summarySheetsPATs: no visible global function definition for
‘image’
pipeline.summarySheetsPATs: no visible global function definition for
‘box’
pipeline.summarySheetsPATs: no visible binding for global variable
‘group.labels’
pipeline.summarySheetsPATs: no visible global function definition for
‘pie’
pipeline.summarySheetsPATs: no visible binding for global variable
‘groupwise.group.colors’
pipeline.summarySheetsPATs: no visible global function definition for
‘mtext’
pipeline.summarySheetsPATs : <anonymous>: no visible binding for global
variable ‘group.labels’
pipeline.summarySheetsPATs: no visible global function definition for
‘barplot’
pipeline.summarySheetsPATs: no visible global function definition for
‘legend’
pipeline.summarySheetsPATs : <anonymous>: no visible binding for global
variable ‘pat.labels’
pipeline.summarySheetsPATs: no visible global function definition for
‘dev.off’
pipeline.summarySheetsSamples: no visible binding for global variable
‘output.paths’
pipeline.summarySheetsSamples: no visible binding for global variable
‘preferences’
pipeline.summarySheetsSamples: no visible binding for global variable
‘gs.def.list’
pipeline.summarySheetsSamples: no visible binding for global variable
‘gene.ids’
pipeline.summarySheetsSamples: no visible binding for global variable
‘indata’
pipeline.summarySheetsSamples: no visible global function definition
for ‘hist’
pipeline.summarySheetsSamples: no visible binding for global variable
‘p.g.m’
pipeline.summarySheetsSamples: no visible global function definition
for ‘pdf’
pipeline.summarySheetsSamples: no visible global function definition
for ‘layout’
pipeline.summarySheetsSamples: no visible global function definition
for ‘par’
pipeline.summarySheetsSamples: no visible global function definition
for ‘text’
pipeline.summarySheetsSamples: no visible binding for global variable
‘perc.DE.m’
pipeline.summarySheetsSamples: no visible binding for global variable
‘fdr.g.m’
pipeline.summarySheetsSamples: no visible binding for global variable
‘t.g.m’
pipeline.summarySheetsSamples: no visible global function definition
for ‘image’
pipeline.summarySheetsSamples: no visible binding for global variable
‘metadata’
pipeline.summarySheetsSamples: no visible global function definition
for ‘color.palette.portraits’
pipeline.summarySheetsSamples: no visible global function definition
for ‘axis’
pipeline.summarySheetsSamples: no visible global function definition
for ‘box’
pipeline.summarySheetsSamples: no visible global function definition
for ‘rect’
pipeline.summarySheetsSamples: no visible binding for global variable
‘gene.coordinates’
pipeline.summarySheetsSamples: no visible binding for global variable
‘gene.descriptions’
pipeline.summarySheetsSamples: no visible global function definition
for ‘mtext’
pipeline.summarySheetsSamples: no visible global function definition
for ‘abline’
pipeline.summarySheetsSamples: no visible binding for global variable
‘n.0.m’
pipeline.summarySheetsSamples: no visible global function definition
for ‘lines’
pipeline.summarySheetsSamples: no visible binding for global variable
‘Fdr.g.m’
pipeline.summarySheetsSamples: no visible global function definition
for ‘legend’
pipeline.summarySheetsSamples: no visible binding for global variable
‘spot.list.samples’
pipeline.summarySheetsSamples: no visible global function definition
for ‘dev.off’
pipeline.supportingMaps: no visible binding for global variable
‘files.name’
pipeline.supportingMaps: no visible global function definition for
‘pdf’
pipeline.supportingMaps: no visible global function definition for
‘par’
pipeline.supportingMaps: no visible binding for global variable
‘som.result’
pipeline.supportingMaps: no visible global function definition for
‘image’
pipeline.supportingMaps: no visible binding for global variable
‘preferences’
pipeline.supportingMaps: no visible global function definition for
‘color.palette.heatmaps’
pipeline.supportingMaps: no visible global function definition for
‘mtext’
pipeline.supportingMaps: no visible global function definition for
‘box’
pipeline.supportingMaps: no visible global function definition for
‘layout’
pipeline.supportingMaps: no visible global function definition for
‘axis’
pipeline.supportingMaps: no visible binding for global variable
‘metadata’
pipeline.supportingMaps: no visible binding for global variable ‘var’
pipeline.supportingMaps: no visible binding for global variable ‘p.m’
pipeline.supportingMaps: no visible global function definition for
‘colorRampPalette’
pipeline.supportingMaps: no visible global function definition for
‘quantile’
pipeline.supportingMaps : <anonymous>: no visible global function
definition for ‘hist’
pipeline.supportingMaps : <anonymous>: no visible binding for global
variable ‘indata’
pipeline.supportingMaps: no visible binding for global variable
‘som.nodes’
pipeline.supportingMaps: no visible global function definition for
‘cor’
pipeline.supportingMaps: no visible binding for global variable
‘indata’
pipeline.supportingMaps : <anonymous>: no visible binding for global
variable ‘metadata’
pipeline.supportingMaps : <anonymous>: no visible binding for global
variable ‘preferences’
pipeline.supportingMaps: no visible global function definition for
‘dev.off’
pipeline.topologyProfiles: no visible binding for global variable
‘metadata’
pipeline.topologyProfiles: no visible binding for global variable
‘files.name’
pipeline.topologyProfiles: no visible binding for global variable
‘group.labels’
pipeline.topologyProfiles: no visible global function definition for
‘pdf’
pipeline.topologyProfiles: no visible global function definition for
‘par’
pipeline.topologyProfiles: no visible binding for global variable
‘preferences’
pipeline.topologyProfiles: no visible global function definition for
‘sd’
pipeline.topologyProfiles: no visible global function definition for
‘barplot’
pipeline.topologyProfiles: no visible binding for global variable
‘group.colors’
pipeline.topologyProfiles: no visible binding for global variable
‘indata’
pipeline.topologyProfiles: no visible global function definition for
‘box’
pipeline.topologyProfiles: no visible global function definition for
‘boxplot’
pipeline.topologyProfiles: no visible binding for global variable
‘groupwise.group.colors’
pipeline.topologyProfiles: no visible global function definition for
‘axis’
pipeline.topologyProfiles : <anonymous>: no visible global function
definition for ‘hist’
pipeline.topologyProfiles : <anonymous>: no visible binding for global
variable ‘group.labels’
pipeline.topologyProfiles : <anonymous>: no visible binding for global
variable ‘preferences’
pipeline.topologyProfiles: no visible global function definition for
‘dev.off’
radarchart: no visible global function definition for ‘polygon’
radarchart: no visible global function definition for ‘text’
radarchart: no visible global function definition for ‘arrows’
radarchart: no visible global function definition for ‘points’
smoothScatter: no visible global function definition for
‘colorRampPalette’
smoothScatter: no visible binding for global variable ‘blues9’
smoothScatter: no visible binding for global variable ‘box’
smoothScatter: no visible global function definition for ‘par’
smoothScatter: no visible global function definition for ‘xy.coords’
smoothScatter: no visible global function definition for ‘image’
smoothScatter: no visible global function definition for ‘points’
util.cat: no visible global function definition for ‘flush.console’
Undefined global functions or variables:
Fdr.g.m WAD.g.m abline aov arrows as.dendrogram axis barplot blues9
bmp box boxplot chull col2rgb color.palette.heatmaps
color.palette.portraits colorRampPalette combn cor cutree data
density dev.off dist ecdf fdr.g.m files.name fisher.test
flush.console frame gene.coordinates gene.descriptions gene.ids
gene.names gene.positions gene.positions.list gene.positions.table
group.colors group.labels group.silhouette.coef
groupwise.group.colors gs.def.list hclust head hist image indata
indata.gene.mean indata.sample.mean kmeans layout legend lines
metadata metagene.filter.list modifyList mtext n.0.m na.omit
opossom.genesets opt.cluster.number order.dendrogram output.paths
p.g.m p.m par parSapply pat.labels pbeta pdf perc.DE.m persp pie
points polygon preferences pt quantile rect reorder rgb
samples.GSZ.scores sd secLvlSom.20.20 secLvlSom.custom sessionInfo
som.nodes som.result spot.list.correlation spot.list.dmap
spot.list.group.overexpression spot.list.kmeans
spot.list.overexpression spot.list.samples spot.list.underexpression
stars t.ensID.m t.g.m t.m text title unique.protein.ids var
wilcox.test write.csv2 xy.coords
Consider adding
importFrom("grDevices", "blues9", "bmp", "chull", "col2rgb",
"colorRampPalette", "dev.off", "pdf", "rgb", "xy.coords")
importFrom("graphics", "abline", "arrows", "axis", "barplot", "box",
"boxplot", "frame", "hist", "image", "layout", "legend",
"lines", "mtext", "par", "persp", "pie", "points",
"polygon", "rect", "stars", "text", "title")
importFrom("stats", "aov", "as.dendrogram", "cor", "cutree", "density",
"dist", "ecdf", "fisher.test", "hclust", "kmeans",
"na.omit", "order.dendrogram", "pbeta", "pt", "quantile",
"reorder", "sd", "var", "wilcox.test")
importFrom("utils", "combn", "data", "flush.console", "head",
"modifyList", "sessionInfo", "write.csv2")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
oposSOM-package 23.057 0.242 36.385
opossom.run 7.121 0.113 31.194
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.3-bioc/meat/oposSOM.Rcheck/00check.log’
for details.