oposSOM 1.4.0
Henry Wirth
| Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/oposSOM | | Last Changed Rev: 105622 / Revision: 109384 | | Last Changed Date: 2015-06-29 07:08:29 -0700 (Mon, 29 Jun 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ WARNINGS ] | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | WARNINGS | OK | |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | WARNINGS | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings oposSOM_1.4.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/oposSOM.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.4.0’
* 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 ... [7s/7s] WARNING
Found the following significant warnings:
Warning: replacing previous import by ‘igraph::normalize’ when loading ‘oposSOM’
See ‘/home/biocbuild/bbs-3.1-bioc/meat/oposSOM.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘grDevices:::.smoothScatterCalcDensity’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
pipeline.2ndLvlComponentAnalysis: no visible binding for global
variable ‘files.name’
pipeline.2ndLvlComponentAnalysis: no visible binding for global
variable ‘metagene.filter.list’
pipeline.2ndLvlComponentAnalysis: no visible binding for global
variable ‘metadata’
pipeline.2ndLvlComponentAnalysis: no visible binding for global
variable ‘group.colors’
pipeline.2ndLvlComponentAnalysis: no visible binding for global
variable ‘group.labels’
pipeline.2ndLvlComponentAnalysis: no visible binding for global
variable ‘groupwise.group.colors’
pipeline.2ndLvlComponentAnalysis: no visible binding for global
variable ‘indata’
pipeline.2ndLvlCorrelationAnalysis: no visible binding for global
variable ‘groupwise.group.colors’
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 binding for global
variable ‘metagene.filter.list’
pipeline.2ndLvlCorrelationAnalysis: no visible binding for global
variable ‘metadata’
pipeline.2ndLvlCorrelationAnalysis: no visible binding for global
variable ‘indata’
pipeline.2ndLvlCorrelationAnalysis: no visible global function
definition for ‘colramp’
pipeline.2ndLvlCorrelationAnalysis : <anonymous>: no visible binding
for global variable ‘group.labels’
pipeline.2ndLvlModuleCorrelation: no visible binding for global
variable ‘indata’
pipeline.2ndLvlModuleCorrelation: no visible binding for global
variable ‘group.colors’
pipeline.2ndLvlModuleCorrelation: no visible global function definition
for ‘colramp’
pipeline.2ndLvlModuleCorrelation : <anonymous>: no visible binding for
global variable ‘spot.list.overexpression’
pipeline.2ndLvlModuleCorrelation: no visible binding for global
variable ‘metagene.filter.list’
pipeline.2ndLvlModuleCorrelation: no visible binding for global
variable ‘i’
pipeline.2ndLvlSimilarityAnalysis: no visible binding for '<<-'
assignment to ‘metagene.filter.list’
pipeline.2ndLvlSimilarityAnalysis: no visible binding for global
variable ‘metagene.filter.list’
pipeline.2ndLvlSimilarityAnalysis: no visible binding for global
variable ‘preferences’
pipeline.2ndLvlSimilarityAnalysis: no visible binding for global
variable ‘spot.list.overexpression’
pipeline.2ndLvlSimilarityAnalysis: no visible binding for global
variable ‘metadata’
pipeline.2ndLvlSimilarityAnalysis: no visible binding for global
variable ‘files.name’
pipeline.2ndLvlSimilarityAnalysis: no visible binding for global
variable ‘indata’
pipeline.2ndLvlSimilarityAnalysis: no visible binding for global
variable ‘group.colors’
pipeline.2ndLvlSimilarityAnalysis: no visible 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 ‘colramp’
pipeline.2ndLvlSom: no visible binding for '<<-' assignment to
‘secLvlSom.custom’
pipeline.2ndLvlSom: no visible binding for global variable ‘metadata’
pipeline.2ndLvlSom: no visible binding for global variable
‘preferences’
pipeline.2ndLvlSom: no visible binding for '<<-' assignment to
‘secLvlSom.20.20’
pipeline.2ndLvlSom: no visible binding for global variable
‘secLvlSom.custom’
pipeline.2ndLvlSom: no visible binding for global variable ‘files.name’
pipeline.2ndLvlSom: no visible binding for global variable
‘group.labels’
pipeline.2ndLvlSom: no visible binding for global variable
‘groupwise.group.colors’
pipeline.2ndLvlSom: no visible binding for global variable
‘group.colors’
pipeline.2ndLvlSom: no visible binding for global variable ‘indata’
pipeline.2ndLvlSom: no visible binding for global variable
‘secLvlSom.20.20’
pipeline.2ndLvlSom: no visible global function definition for ‘colramp’
pipeline.3rdLvlChromosomalEnrichment: no visible binding for global
variable ‘output.paths’
pipeline.3rdLvlChromosomalEnrichment: no visible binding for global
variable ‘files.name’
pipeline.3rdLvlChromosomalEnrichment : plot.set.list.chromosomes: no
visible binding for global variable ‘gene.positions’
pipeline.3rdLvlChromosomalEnrichment : plot.set.list.chromosomes: no
visible binding for global variable ‘gene.positions.list’
pipeline.3rdLvlChromosomalEnrichment: no visible binding for global
variable ‘gene.positions.list’
pipeline.3rdLvlChromosomalEnrichment: no visible binding for global
variable ‘spot.list.overexpression’
pipeline.3rdLvlChromosomalEnrichment: no visible binding for global
variable ‘spot.list.underexpression’
pipeline.3rdLvlChromosomalEnrichment: no visible binding for global
variable ‘spot.list.kmeans’
pipeline.3rdLvlChromosomalEnrichment: no visible binding for global
variable ‘group.labels’
pipeline.3rdLvlChromosomalEnrichment: no visible binding for global
variable ‘spot.list.group.overexpression’
pipeline.3rdLvlNetworks : plot.set.list.networks: no visible binding
for global variable ‘metadata’
pipeline.3rdLvlNetworks : plot.set.list.networks: no visible binding
for global variable ‘preferences’
pipeline.3rdLvlNetworks: no visible binding for global variable
‘files.name’
pipeline.3rdLvlNetworks: no visible binding for global variable
‘spot.list.overexpression’
pipeline.3rdLvlNetworks: no visible binding for global variable
‘spot.list.underexpression’
pipeline.3rdLvlNetworks: no visible binding for global variable
‘spot.list.kmeans’
pipeline.3rdLvlNetworks: no visible binding for global variable
‘group.labels’
pipeline.3rdLvlNetworks: no visible binding for global variable
‘spot.list.group.overexpression’
pipeline.3rdLvlSummarySheets : plot.set.list.reports: no visible
binding for global variable ‘group.labels’
pipeline.3rdLvlSummarySheets : plot.set.list.reports: no visible
binding for global variable ‘metadata’
pipeline.3rdLvlSummarySheets : plot.set.list.reports: no visible
binding for global variable ‘preferences’
pipeline.3rdLvlSummarySheets : plot.set.list.reports: no visible global
function definition for ‘colramp’
pipeline.3rdLvlSummarySheets : plot.set.list.reports: no visible
binding for global variable ‘group.colors’
pipeline.3rdLvlSummarySheets : plot.set.list.reports: no visible
binding for global variable ‘indata’
pipeline.3rdLvlSummarySheets : plot.set.list.reports: no visible
binding for global variable ‘groupwise.group.colors’
pipeline.3rdLvlSummarySheets : plot.set.list.reports : <anonymous>: no
visible binding for global variable ‘group.labels’
pipeline.3rdLvlSummarySheets : plot.set.list.reports: no visible
binding for global variable ‘spot.list.samples’
pipeline.3rdLvlSummarySheets: no visible binding for global variable
‘files.name’
pipeline.3rdLvlSummarySheets: no visible binding for global variable
‘spot.list.overexpression’
pipeline.3rdLvlSummarySheets: no visible binding for global variable
‘spot.list.underexpression’
pipeline.3rdLvlSummarySheets: no visible binding for global variable
‘spot.list.kmeans’
pipeline.3rdLvlSummarySheets: no visible binding for global variable
‘group.labels’
pipeline.3rdLvlSummarySheets: no visible binding for global variable
‘spot.list.group.overexpression’
pipeline.affymetrixQualityCheck: no visible binding for global variable
‘indata’
pipeline.affymetrixQualityCheck: no visible binding for global variable
‘group.colors’
pipeline.affymetrixQualityCheck: no visible binding for global variable
‘group.labels’
pipeline.affymetrixQualityCheck: no visible binding for global variable
‘groupwise.group.colors’
pipeline.calcStatistics: no visible binding for global variable
‘output.paths’
pipeline.calcStatistics: no visible binding for global variable
‘preferences’
pipeline.calcStatistics: no visible binding for global variable
‘indata.original’
pipeline.calcStatistics: no visible binding for global variable
‘indata’
pipeline.calcStatistics: no visible binding for '<<-' assignment to
‘sd.g.m’
pipeline.calcStatistics: no visible binding for '<<-' assignment to
‘WAD.g.m’
pipeline.calcStatistics: no visible binding for '<<-' assignment to
‘t.g.m’
pipeline.calcStatistics: no visible binding for '<<-' assignment to
‘p.g.m’
pipeline.calcStatistics: no visible binding for '<<-' assignment to
‘n.0.m’
pipeline.calcStatistics: no visible binding for global variable ‘n.0.m’
pipeline.calcStatistics: no visible binding for '<<-' assignment to
‘perc.DE.m’
pipeline.calcStatistics: no visible binding for global variable
‘perc.DE.m’
pipeline.calcStatistics: no visible binding for '<<-' assignment to
‘fdr.g.m’
pipeline.calcStatistics: no visible binding for '<<-' assignment to
‘Fdr.g.m’
pipeline.calcStatistics: no visible binding for global variable
‘WAD.g.m’
pipeline.calcStatistics : <anonymous>: no visible binding for global
variable ‘indata.original’
pipeline.calcStatistics: no visible binding for global variable
‘sd.g.m’
pipeline.calcStatistics: no visible binding for global variable ‘t.g.m’
pipeline.calcStatistics : <anonymous>: no visible binding for global
variable ‘sd.g.m’
pipeline.calcStatistics: no visible binding for global variable
‘group.labels’
pipeline.calcStatistics : <anonymous>: no visible binding for global
variable ‘group.labels’
pipeline.calcStatistics: no visible binding for global variable ‘p.g.m’
pipeline.calcStatistics: no visible binding for global variable
‘fdr.g.m’
pipeline.calcStatistics: no visible binding for global variable
‘Fdr.g.m’
pipeline.calcStatistics: no visible binding for '<<-' assignment to
‘t.m’
pipeline.calcStatistics: no visible binding for '<<-' assignment to
‘p.m’
pipeline.calcStatistics: no visible binding for '<<-' assignment to
‘fdr.m’
pipeline.calcStatistics: no visible binding for global variable
‘som.nodes’
pipeline.calcStatistics: no visible binding for global variable ‘t.m’
pipeline.calcStatistics: no visible binding for global variable ‘p.m’
pipeline.calcStatistics: no visible binding for global variable ‘fdr.m’
pipeline.calcStatistics: no visible binding for global variable
‘group.colors’
pipeline.cancerHallmarks : <anonymous>: no visible binding for global
variable ‘gs.def.list’
pipeline.cancerHallmarks : <anonymous>: no visible binding for global
variable ‘gene.ids’
pipeline.cancerHallmarks: no visible binding for global variable
‘indata’
pipeline.cancerHallmarks : <anonymous>: no visible binding for global
variable ‘unique.protein.ids’
pipeline.cancerHallmarks : <anonymous>: no visible binding for global
variable ‘t.ensID.m’
pipeline.cancerHallmarks: no visible binding for global variable
‘spot.list.overexpression’
pipeline.cancerHallmarks: no visible binding for global variable
‘files.name’
pipeline.cancerHallmarks: no visible binding for global variable
‘group.labels’
pipeline.cancerHallmarks: no visible binding for global variable
‘groupwise.group.colors’
pipeline.cancerHallmarks: no visible binding for global variable
‘preferences’
pipeline.cancerHallmarks: no visible binding for global variable
‘som.nodes’
pipeline.cancerHallmarks: no visible global function definition for
‘colramp’
pipeline.chromosomeExpressionReports: no visible binding for global
variable ‘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 binding for global
variable ‘group.colors’
pipeline.detectEnsemblDataset: no visible binding for '<<-' assignment
to ‘preferences’
pipeline.detectEnsemblDataset: no visible binding for global variable
‘preferences’
pipeline.detectEnsemblDataset: no visible binding for global variable
‘indata’
pipeline.detectSpotsIntegral: no visible binding for global variable
‘metadata’
pipeline.detectSpotsIntegral: no visible binding for global variable
‘indata’
pipeline.detectSpotsIntegral: no visible binding for global variable
‘preferences’
pipeline.detectSpotsIntegral: no visible binding for '<<-' assignment
to ‘spot.list.overexpression’
pipeline.detectSpotsIntegral: no visible binding for global variable
‘spot.list.overexpression’
pipeline.detectSpotsIntegral: no visible binding for global variable
‘som.nodes’
pipeline.detectSpotsIntegral: no visible binding for global variable
‘som.result’
pipeline.detectSpotsIntegral : <anonymous>: no visible binding for
global variable ‘metadata’
pipeline.detectSpotsIntegral : <anonymous>: no visible binding for
global variable ‘indata’
pipeline.detectSpotsIntegral: no visible binding for '<<-' assignment
to ‘spot.list.underexpression’
pipeline.detectSpotsIntegral: no visible binding for global variable
‘spot.list.underexpression’
pipeline.detectSpotsIntegral: no visible binding for '<<-' assignment
to ‘spot.list.correlation’
pipeline.detectSpotsIntegral: no visible binding for global variable
‘spot.list.correlation’
pipeline.detectSpotsIntegral: no visible binding for '<<-' assignment
to ‘spot.list.kmeans’
pipeline.detectSpotsIntegral: no visible binding for global variable
‘spot.list.kmeans’
pipeline.detectSpotsIntegral: no visible binding for global variable
‘group.labels’
pipeline.detectSpotsIntegral: no visible binding for global variable
‘group.metadata’
pipeline.detectSpotsIntegral: no visible binding for '<<-' assignment
to ‘spot.list.group.overexpression’
pipeline.detectSpotsIntegral: no visible binding for global variable
‘spot.list.group.overexpression’
pipeline.detectSpotsIntegral : <anonymous>: no visible binding for
global variable ‘group.metadata’
pipeline.detectSpotsIntegral : <anonymous>: no visible binding for
global variable ‘preferences’
pipeline.detectSpotsSamples: no visible binding for '<<-' assignment to
‘spot.list.samples’
pipeline.detectSpotsSamples: no visible binding for global variable
‘indata’
pipeline.detectSpotsSamples: no visible binding for global variable
‘spot.list.samples’
pipeline.detectSpotsSamples: no visible binding for global variable
‘preferences’
pipeline.detectSpotsSamples: no visible binding for global variable
‘metadata’
pipeline.detectSpotsSamples: no visible binding for global variable
‘som.nodes’
pipeline.differenceAnalyses: no visible binding for global variable
‘group.labels’
pipeline.differenceAnalyses : <anonymous>: no visible binding for
global variable ‘group.labels’
pipeline.differenceAnalyses: no visible binding for global variable
‘preferences’
pipeline.differenceAnalyses: no visible binding for global variable
‘files.name’
pipeline.differenceAnalyses: no visible binding for '<<-' assignment to
‘WAD.g.m’
pipeline.differenceAnalyses: no visible binding for global variable
‘indata’
pipeline.differenceAnalyses: no visible binding for '<<-' assignment to
‘t.g.m’
pipeline.differenceAnalyses: no visible binding for '<<-' assignment to
‘p.g.m’
pipeline.differenceAnalyses: no visible binding for '<<-' assignment to
‘fdr.g.m’
pipeline.differenceAnalyses: no visible binding for '<<-' assignment to
‘Fdr.g.m’
pipeline.differenceAnalyses: no visible binding for '<<-' assignment to
‘n.0.m’
pipeline.differenceAnalyses: no visible binding for global variable
‘n.0.m’
pipeline.differenceAnalyses: no visible binding for '<<-' assignment to
‘perc.DE.m’
pipeline.differenceAnalyses: no visible binding for global variable
‘perc.DE.m’
pipeline.differenceAnalyses: no visible binding for '<<-' assignment to
‘indata’
pipeline.differenceAnalyses: no visible binding for '<<-' assignment to
‘metadata’
pipeline.differenceAnalyses: no visible binding for global variable
‘metadata’
pipeline.differenceAnalyses: no visible binding for global variable
‘indata.original’
pipeline.differenceAnalyses: no visible binding for global variable
‘t.g.m’
pipeline.differenceAnalyses: no visible binding for global variable
‘p.g.m’
pipeline.differenceAnalyses: no visible binding for global variable
‘fdr.g.m’
pipeline.differenceAnalyses: no visible binding for global variable
‘Fdr.g.m’
pipeline.differenceAnalyses: no visible binding for global variable
‘WAD.g.m’
pipeline.differenceAnalyses: no visible binding for '<<-' assignment to
‘group.labels’
pipeline.differenceAnalyses: no visible binding for '<<-' assignment to
‘group.colors’
pipeline.differenceAnalyses: no visible binding for global variable
‘group.colors’
pipeline.differenceAnalyses: no visible binding for '<<-' assignment to
‘output.paths’
pipeline.entropyProfiles: no visible binding for global variable
‘files.name’
pipeline.entropyProfiles: no visible binding for global variable
‘metadata’
pipeline.entropyProfiles: no visible binding for global variable
‘group.colors’
pipeline.entropyProfiles: no visible binding for global variable
‘indata’
pipeline.entropyProfiles: no visible binding for global variable
‘group.labels’
pipeline.entropyProfiles: no visible binding for global variable
‘groupwise.group.colors’
pipeline.entropyProfiles : <anonymous>: no visible binding for global
variable ‘preferences’
pipeline.entropyProfiles: no visible binding for global variable
‘som.result’
pipeline.geneLists: no visible binding for global variable ‘metadata’
pipeline.geneLists: no visible binding for global variable
‘output.paths’
pipeline.geneLists: no visible binding for global variable ‘indata’
pipeline.geneLists: no visible binding for global variable ‘p.g.m’
pipeline.geneLists: no visible binding for global variable ‘gene.names’
pipeline.geneLists: no visible binding for global variable ‘files.name’
pipeline.geneLists: no visible binding for global variable
‘gs.def.list’
pipeline.geneLists: no visible binding for global variable ‘WAD.g.m’
pipeline.geneLists: no visible binding for global variable ‘t.g.m’
pipeline.geneLists: no visible binding for global variable ‘fdr.g.m’
pipeline.geneLists: no visible binding for global variable ‘Fdr.g.m’
pipeline.geneLists: no visible binding for global variable
‘gene.coordinates’
pipeline.geneLists: no visible binding for global variable
‘gene.positions’
pipeline.geneLists: no visible binding for global variable
‘gene.descriptions’
pipeline.geneLists: no visible binding for global variable ‘perc.DE.m’
pipeline.geneLists: no visible binding for global variable
‘spot.list.samples’
pipeline.geneLists: no visible binding for global variable
‘preferences’
pipeline.genesetOverviews: no visible binding for global variable
‘files.name’
pipeline.genesetOverviews: no visible binding for global variable
‘spot.list.overexpression’
pipeline.genesetOverviews : <anonymous>: no visible binding for global
variable ‘gs.def.list’
pipeline.genesetOverviews: no visible binding for global variable
‘gs.def.list.categories’
pipeline.genesetOverviews: no visible binding for global variable
‘samples.GSZ.scores’
pipeline.genesetOverviews: no visible binding for global variable
‘indata’
pipeline.genesetOverviews: no visible binding for global variable
‘group.colors’
pipeline.genesetOverviews: no visible binding for global variable
‘group.labels’
pipeline.genesetOverviews : <anonymous>: no visible binding for global
variable ‘group.labels’
pipeline.genesetOverviews: no visible binding for global variable
‘preferences’
pipeline.genesetOverviews: no visible binding for global variable
‘spot.list.samples’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
‘samples.GSZ.scores’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
‘gs.def.list’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
‘files.name’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
‘group.colors’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
‘indata’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
‘group.labels’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
‘groupwise.group.colors’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
‘spot.list.overexpression’
pipeline.genesetProfilesAndMaps : <anonymous>: no visible binding for
global variable ‘gs.def.list’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
‘spot.list.kmeans’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
‘gene.ids’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
‘gene.coordinates’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
‘gene.names’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
‘gene.descriptions’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
‘preferences’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
‘som.nodes’
pipeline.genesetProfilesAndMaps: no visible global function definition
for ‘colramp’
pipeline.genesetProfilesAndMaps: no visible binding for global variable
‘som.result’
pipeline.genesetStatisticIntegral : spot.fisher.p: no visible binding
for global variable ‘gene.ids’
pipeline.genesetStatisticIntegral : spot.fisher.p: no visible binding
for global variable ‘unique.protein.ids’
pipeline.genesetStatisticIntegral : spot.fisher.p: no visible binding
for global variable ‘gs.def.list’
pipeline.genesetStatisticIntegral: no visible binding for '<<-'
assignment to ‘spot.list.overexpression’
pipeline.genesetStatisticIntegral: no visible binding for global
variable ‘spot.list.overexpression’
pipeline.genesetStatisticIntegral: no visible binding for '<<-'
assignment to ‘spot.list.underexpression’
pipeline.genesetStatisticIntegral: no visible binding for global
variable ‘spot.list.underexpression’
pipeline.genesetStatisticIntegral: no visible binding for global
variable ‘spot.list.correlation’
pipeline.genesetStatisticIntegral: no visible binding for '<<-'
assignment to ‘spot.list.correlation’
pipeline.genesetStatisticIntegral: no visible binding for '<<-'
assignment to ‘spot.list.kmeans’
pipeline.genesetStatisticIntegral: no visible binding for global
variable ‘spot.list.kmeans’
pipeline.genesetStatisticIntegral: no visible binding for global
variable ‘group.labels’
pipeline.genesetStatisticIntegral: no visible binding for '<<-'
assignment to ‘spot.list.group.overexpression’
pipeline.genesetStatisticIntegral: no visible binding for global
variable ‘spot.list.group.overexpression’
pipeline.genesetStatisticSamples: no visible binding for global
variable ‘indata’
pipeline.genesetStatisticSamples: no visible binding for '<<-'
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 : <anonymous>: no visible binding for
global variable ‘spot.list.samples’
pipeline.genesetStatisticSamples : <anonymous>: no visible binding for
global variable ‘gene.ids’
pipeline.genesetStatisticSamples: no visible binding for '<<-'
assignment to ‘spot.list.samples’
pipeline.genesetStatisticSamples: no visible binding for global
variable ‘spot.list.samples’
pipeline.genesetStatisticSamples : <anonymous>: no visible binding for
global variable ‘gs.def.list’
pipeline.genesetStatisticSamples : <anonymous>: no visible binding for
global variable ‘preferences’
pipeline.genesetStatisticSamples: no visible binding for '<<-'
assignment to ‘samples.GSZ.scores’
pipeline.genesetStatisticSamples: no visible binding for global
variable ‘files.name’
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 global variable
‘preferences’
pipeline.groupAnalysis: no visible binding for '<<-' assignment to
‘metadata’
pipeline.groupAnalysis: no visible binding for global variable
‘metadata’
pipeline.groupAnalysis: no visible binding for '<<-' assignment to
‘indata.original’
pipeline.groupAnalysis: no visible binding for global variable
‘indata.original’
pipeline.groupAnalysis: no visible binding for '<<-' assignment to
‘indata’
pipeline.groupAnalysis: no visible binding for '<<-' assignment to
‘indata.gene.mean’
pipeline.groupAnalysis: no visible binding for global variable ‘indata’
pipeline.groupAnalysis: no visible binding for global variable
‘indata.gene.mean’
pipeline.groupAnalysis: no visible binding for '<<-' assignment to
‘group.colors’
pipeline.groupAnalysis: no visible binding for global variable
‘group.colors’
pipeline.groupAnalysis: no visible binding for '<<-' assignment to
‘group.labels’
pipeline.groupAnalysis: no visible binding for '<<-' assignment to
‘output.paths’
pipeline.groupAnalysis: no visible binding for '<<-' assignment to
‘preferences’
pipeline.groupAssignment: no visible binding for global variable
‘group.labels’
pipeline.groupAssignment: no visible binding for '<<-' assignment to
‘group.silhouette.coef’
pipeline.groupAssignment: no visible binding for global variable
‘indata’
pipeline.groupAssignment: no visible binding for global variable
‘metadata’
pipeline.groupAssignment : <anonymous>: no visible binding for global
variable ‘group.labels’
pipeline.groupAssignment: no visible binding for global variable
‘group.silhouette.coef’
pipeline.groupSpecificGenesets: no visible binding for global variable
‘group.labels’
pipeline.groupSpecificGenesets: no visible binding for global variable
‘spot.list.samples’
pipeline.groupSpecificGenesets : <anonymous>: no visible binding for
global variable ‘gs.def.list’
pipeline.groupSpecificGenesets : <anonymous>: no visible binding for
global variable ‘group.labels’
pipeline.groupSpecificGenesets: no visible binding for global variable
‘files.name’
pipeline.groupSpecificGenesets: no visible binding for global variable
‘group.colors’
pipeline.groupSpecificGenesets: no visible binding for global variable
‘indata’
pipeline.groupSpecificGenesets: no visible binding for global variable
‘preferences’
pipeline.groupSpecificGenesets: no visible binding for global variable
‘som.nodes’
pipeline.groupSpecificGenesets: no visible binding for global variable
‘gene.ids’
pipeline.groupSpecificGenesets: no visible binding for global variable
‘gs.def.list’
pipeline.groupSpecificGenesets: no visible global function definition
for ‘colramp’
pipeline.htmlDifferencesSummary: no visible binding for global variable
‘files.name’
pipeline.htmlDifferencesSummary: no visible binding for global variable
‘indata’
pipeline.htmlDifferencesSummary: no visible binding for global variable
‘spot.list.samples’
pipeline.htmlGenesetAnalysis: no visible binding for global variable
‘preferences’
pipeline.htmlGenesetAnalysis: no visible binding for global variable
‘files.name’
pipeline.htmlGenesetAnalysis: no visible binding for global variable
‘gs.def.list’
pipeline.htmlGenesetAnalysis: no visible binding for global variable
‘gs.def.list.categories’
pipeline.htmlGroupSummary: no visible binding for global variable
‘group.labels’
pipeline.htmlGroupSummary: no visible binding for global variable
‘files.name’
pipeline.htmlGroupSummary: no visible binding for global variable
‘preferences’
pipeline.htmlGroupSummary: no visible binding for global variable
‘indata’
pipeline.htmlGroupSummary: no visible binding for global variable
‘spot.list.samples’
pipeline.htmlIntegralSummary: no visible binding for global variable
‘files.name’
pipeline.htmlIntegralSummary: no visible binding for global variable
‘spot.list.overexpression’
pipeline.htmlIntegralSummary: no visible binding for global variable
‘group.labels’
pipeline.htmlIntegralSummary: no visible binding for global variable
‘spot.list.group.overexpression’
pipeline.htmlIntegralSummary: no visible binding for global variable
‘spot.list.underexpression’
pipeline.htmlIntegralSummary: no visible binding for global variable
‘spot.list.correlation’
pipeline.htmlIntegralSummary: no visible binding for global variable
‘spot.list.kmeans’
pipeline.htmlSampleSummary: no visible binding for global variable
‘files.name’
pipeline.htmlSampleSummary: no visible binding for global variable
‘group.labels’
pipeline.htmlSampleSummary: no visible binding for global variable
‘indata’
pipeline.htmlSampleSummary: no visible binding for global variable
‘spot.list.samples’
pipeline.htmlSummary: no visible binding for global variable
‘files.name’
pipeline.htmlSummary: no visible binding for global variable ‘indata’
pipeline.htmlSummary: no visible binding for global variable
‘group.labels’
pipeline.htmlSummary: no visible binding for global variable
‘preferences’
pipeline.prepare: no visible binding for global variable ‘preferences’
pipeline.prepare: no visible binding for '<<-' assignment to
‘preferences’
pipeline.prepare : <anonymous>: no visible binding for global variable
‘indata’
pipeline.prepare: no visible binding for global variable ‘indata’
pipeline.prepare: no visible binding for '<<-' assignment to
‘group.labels’
pipeline.prepare: no visible binding for '<<-' assignment to
‘group.colors’
pipeline.prepare: no visible binding for '<<-' assignment to ‘indata’
pipeline.prepare: no visible binding for global variable ‘group.labels’
pipeline.prepare: no visible binding for global variable ‘group.colors’
pipeline.prepare: no visible binding for global variable
‘indata.original’
pipeline.prepare: no visible binding for '<<-' assignment to
‘indata.original’
pipeline.prepare: no visible binding for '<<-' assignment to
‘files.name’
pipeline.prepare: no visible binding for global variable ‘files.name’
pipeline.prepare: no visible binding for '<<-' assignment to
‘output.paths’
pipeline.prepare: no visible binding for global variable ‘colramp’
pipeline.prepare: no visible binding for '<<-' assignment to ‘colramp’
pipeline.prepare: no visible global function definition for ‘colramp’
pipeline.prepare: no visible binding for '<<-' assignment to
‘groupwise.group.colors’
pipeline.prepare: no visible binding for global variable
‘groupwise.group.colors’
pipeline.prepare: no visible binding for '<<-' assignment to
‘indata.sample.mean’
pipeline.prepare: no visible binding for global variable
‘indata.sample.mean’
pipeline.prepare: no visible binding for '<<-' assignment to
‘indata.gene.mean’
pipeline.prepare: no visible binding for global variable
‘indata.gene.mean’
pipeline.prepare: no visible binding for '<<-' assignment to
‘som.result’
pipeline.prepare: no visible binding for global variable ‘som.result’
pipeline.prepare: no visible binding for '<<-' assignment to ‘metadata’
pipeline.prepare: no visible binding for global variable ‘metadata’
pipeline.prepare: no visible binding for '<<-' assignment to
‘loglog.metadata’
pipeline.prepare: no visible binding for '<<-' assignment to
‘WAD.metadata’
pipeline.prepare: no visible binding for '<<-' assignment to
‘group.metadata’
pipeline.prepare: no visible binding for '<<-' assignment to
‘loglog.group.metadata’
pipeline.prepare: no visible binding for global variable
‘loglog.metadata’
pipeline.prepare: no visible binding for '<<-' assignment to
‘WAD.group.metadata’
pipeline.prepare: no visible binding for global variable ‘WAD.metadata’
pipeline.prepare: no visible binding for '<<-' assignment to
‘gene.coordinates’
pipeline.prepare: no visible binding for global variable
‘gene.coordinates’
pipeline.prepare: no visible binding for '<<-' assignment to
‘som.nodes’
pipeline.prepare: no visible binding for global variable ‘som.nodes’
pipeline.prepareAnnotation: no visible binding for '<<-' assignment to
‘gene.ids’
pipeline.prepareAnnotation: no visible binding for global variable
‘indata’
pipeline.prepareAnnotation: no visible binding for global variable
‘gene.ids’
pipeline.prepareAnnotation: no visible binding for '<<-' assignment to
‘gene.names’
pipeline.prepareAnnotation: no visible binding for global variable
‘gene.names’
pipeline.prepareAnnotation: no visible binding for '<<-' assignment to
‘gene.descriptions’
pipeline.prepareAnnotation: no visible binding for global variable
‘gene.descriptions’
pipeline.prepareAnnotation: no visible binding for '<<-' assignment to
‘gene.positions’
pipeline.prepareAnnotation: no visible binding for global variable
‘gene.positions’
pipeline.prepareAnnotation: no visible binding for '<<-' assignment to
‘gene.positions.table’
pipeline.prepareAnnotation: no visible binding for '<<-' assignment to
‘gene.positions.list’
pipeline.prepareAnnotation: no visible binding for '<<-' assignment to
‘preferences’
pipeline.prepareAnnotation: no visible binding for global variable
‘preferences’
pipeline.prepareAnnotation: no visible binding for global variable
‘gene.positions.table’
pipeline.prepareAnnotation: no visible binding for global variable
‘gene.positions.list’
pipeline.prepareAnnotation : <anonymous>: no visible binding for global
variable ‘gene.positions.table’
pipeline.prepareAnnotation: no visible binding for '<<-' assignment to
‘unique.protein.ids’
pipeline.prepareAnnotation: no visible binding for global variable
‘unique.protein.ids’
pipeline.prepareAnnotation: no visible binding for '<<-' assignment to
‘gs.def.list’
pipeline.prepareAnnotation: no visible binding for global variable
‘gs.def.list’
pipeline.prepareAnnotation : <anonymous>: no visible binding for global
variable ‘gene.ids’
pipeline.prepareAnnotation: no visible binding for global variable
‘opossom.genesets’
pipeline.prepareAnnotation : <anonymous>: no visible binding for global
variable ‘unique.protein.ids’
pipeline.prepareAnnotation: no visible binding for '<<-' assignment to
‘gs.def.list.categories’
pipeline.qualityCheck: no visible binding for global variable
‘output.paths’
pipeline.qualityCheck : plot.poly.density: no visible binding for
global variable ‘indata’
pipeline.qualityCheck: no visible binding for global variable ‘indata’
pipeline.qualityCheck: no visible binding for global variable
‘group.labels’
pipeline.qualityCheck: no visible binding for global variable
‘groupwise.group.colors’
pipeline.qualityCheck: no visible binding for global variable
‘indata.sample.mean’
pipeline.qualityCheck: no visible binding for global variable
‘group.colors’
pipeline.sampleExpressionPortraits: no visible binding for global
variable ‘files.name’
pipeline.sampleExpressionPortraits: no visible binding for global
variable ‘group.labels’
pipeline.sampleExpressionPortraits: no visible binding for global
variable ‘groupwise.group.colors’
pipeline.sampleExpressionPortraits: no visible binding for global
variable ‘metadata’
pipeline.sampleExpressionPortraits: no visible binding for global
variable ‘preferences’
pipeline.sampleExpressionPortraits: no visible global function
definition for ‘colramp’
pipeline.sampleExpressionPortraits: no visible binding for global
variable ‘indata’
pipeline.sampleExpressionPortraits: no visible binding for global
variable ‘group.silhouette.coef’
pipeline.sampleExpressionPortraits: no visible binding for global
variable ‘WAD.metadata’
pipeline.sampleExpressionPortraits: no visible binding for global
variable ‘loglog.metadata’
pipeline.sampleRankMaps: no visible binding for global variable
‘files.name’
pipeline.sampleRankMaps: no visible binding for global variable
‘group.labels’
pipeline.sampleRankMaps: no visible binding for global variable
‘groupwise.group.colors’
pipeline.sampleRankMaps: no visible binding for global variable
‘indata’
pipeline.sampleRankMaps: no visible binding for global variable
‘som.nodes’
pipeline.sampleRankMaps: no visible binding for global variable
‘preferences’
pipeline.sampleRankMaps: no visible global function definition for
‘colramp’
pipeline.sampleRankMaps: no visible binding for global variable
‘WAD.g.m’
pipeline.sampleRankMaps: no visible binding for global variable ‘t.g.m’
pipeline.signatureSets: no visible binding for global variable
‘spot.list.overexpression’
pipeline.signatureSets : <anonymous>: no visible binding for global
variable ‘indata’
pipeline.signatureSets : <anonymous>: no visible binding for global
variable ‘metadata’
pipeline.signatureSets : <anonymous>: no visible binding for global
variable ‘som.nodes’
pipeline.signatureSets: no visible binding for global variable
‘gene.ids’
pipeline.signatureSets: no visible binding for global variable
‘files.name’
pipeline.summarySheetsGroups: no visible binding for global variable
‘metadata’
pipeline.summarySheetsGroups: no visible binding for global variable
‘group.labels’
pipeline.summarySheetsGroups: no visible binding for global variable
‘group.metadata’
pipeline.summarySheetsGroups: no visible binding for global variable
‘WAD.group.metadata’
pipeline.summarySheetsGroups: no visible binding for global variable
‘loglog.group.metadata’
pipeline.summarySheetsGroups: no visible binding for global variable
‘files.name’
pipeline.summarySheetsGroups: no visible binding for global variable
‘groupwise.group.colors’
pipeline.summarySheetsGroups: no visible binding for global variable
‘preferences’
pipeline.summarySheetsGroups: no visible global function definition for
‘colramp’
pipeline.summarySheetsGroups: no visible binding for global variable
‘group.silhouette.coef’
pipeline.summarySheetsGroups : <anonymous>: no visible binding for
global variable ‘group.labels’
pipeline.summarySheetsGroups: no visible binding for global variable
‘indata’
pipeline.summarySheetsGroups: no visible binding for global variable
‘group.colors’
pipeline.summarySheetsGroups : <anonymous>: no visible binding for
global variable ‘groupwise.group.colors’
pipeline.summarySheetsIntegral : plot.set.list: no visible binding for
global variable ‘preferences’
pipeline.summarySheetsIntegral : plot.set.list: no visible global
function definition for ‘colramp’
pipeline.summarySheetsIntegral : plot.set.list: no visible binding for
global variable ‘indata’
pipeline.summarySheetsIntegral : plot.set.list: no visible binding for
global variable ‘metadata’
pipeline.summarySheetsIntegral : plot.set.list: no visible binding for
global variable ‘group.labels’
pipeline.summarySheetsIntegral : plot.set.list: no visible binding for
global variable ‘group.colors’
pipeline.summarySheetsIntegral : plot.set.list: no visible binding for
global variable ‘spot.list.samples’
pipeline.summarySheetsIntegral : plot.set.list : <anonymous>: no
visible binding for global variable ‘indata’
pipeline.summarySheetsIntegral : plot.set.list : <anonymous>: no
visible binding for global variable ‘metadata’
pipeline.summarySheetsIntegral : plot.set.list : <anonymous>: no
visible binding for global variable ‘som.nodes’
pipeline.summarySheetsIntegral : plot.set.list: no visible binding for
global variable ‘gene.names’
pipeline.summarySheetsIntegral : plot.set.list: no visible binding for
global variable ‘gene.descriptions’
pipeline.summarySheetsIntegral : plot.set.list: no visible binding for
global variable ‘gs.def.list’
pipeline.summarySheetsIntegral : plot.set.list : <anonymous>: no
visible binding for global variable ‘gene.ids’
pipeline.summarySheetsIntegral : plot.set.list: no visible binding for
global variable ‘gs.def.list.categories’
pipeline.summarySheetsIntegral : csv.set.list : <anonymous>: no visible
binding for global variable ‘indata’
pipeline.summarySheetsIntegral : csv.set.list : <anonymous>: no visible
binding for global variable ‘metadata’
pipeline.summarySheetsIntegral : csv.set.list : <anonymous>: no visible
binding for global variable ‘som.nodes’
pipeline.summarySheetsIntegral : csv.set.list: no visible binding for
global variable ‘indata’
pipeline.summarySheetsIntegral : csv.set.list: no visible binding for
global variable ‘gene.names’
pipeline.summarySheetsIntegral : csv.set.list: no visible binding for
global variable ‘files.name’
pipeline.summarySheetsIntegral : csv.set.list: no visible binding for
global variable ‘gs.def.list.categories’
pipeline.summarySheetsIntegral : csv.set.list: no visible binding for
global variable ‘indata.gene.mean’
pipeline.summarySheetsIntegral : csv.set.list: no visible binding for
global variable ‘gene.coordinates’
pipeline.summarySheetsIntegral : csv.set.list: no visible binding for
global variable ‘gene.positions’
pipeline.summarySheetsIntegral : csv.set.list: no visible binding for
global variable ‘gene.descriptions’
pipeline.summarySheetsIntegral: no visible binding for global variable
‘output.paths’
pipeline.summarySheetsIntegral: no visible binding for global variable
‘spot.list.overexpression’
pipeline.summarySheetsIntegral: no visible binding for global variable
‘spot.list.underexpression’
pipeline.summarySheetsIntegral: no visible binding for global variable
‘spot.list.correlation’
pipeline.summarySheetsIntegral: no visible binding for global variable
‘spot.list.kmeans’
pipeline.summarySheetsIntegral: no visible binding for global variable
‘group.labels’
pipeline.summarySheetsIntegral: no visible binding for global variable
‘spot.list.group.overexpression’
pipeline.summarySheetsSamples: no visible binding for global variable
‘metadata’
pipeline.summarySheetsSamples: no visible binding for global variable
‘output.paths’
pipeline.summarySheetsSamples: no visible binding for global variable
‘preferences’
pipeline.summarySheetsSamples: no visible binding for global variable
‘gs.def.list’
pipeline.summarySheetsSamples: no visible binding for global variable
‘gene.ids’
pipeline.summarySheetsSamples: no visible binding for global variable
‘indata’
pipeline.summarySheetsSamples: no visible binding for global variable
‘p.g.m’
pipeline.summarySheetsSamples: no visible binding for global variable
‘perc.DE.m’
pipeline.summarySheetsSamples: no visible binding for global variable
‘fdr.g.m’
pipeline.summarySheetsSamples: no visible binding for global variable
‘t.g.m’
pipeline.summarySheetsSamples: no visible global function definition
for ‘colramp’
pipeline.summarySheetsSamples: no visible binding for global variable
‘spot.list.samples’
pipeline.summarySheetsSamples: no visible binding for global variable
‘gene.coordinates’
pipeline.summarySheetsSamples: no visible binding for global variable
‘gene.descriptions’
pipeline.summarySheetsSamples: no visible binding for global variable
‘n.0.m’
pipeline.summarySheetsSamples: no visible binding for global variable
‘Fdr.g.m’
pipeline.summarySheetsSamples: no visible binding for global variable
‘gs.def.list.categories’
pipeline.summarySheetsSamples : <anonymous>: no visible binding for
global variable ‘gene.ids’
pipeline.supportingMaps: no visible binding for global variable
‘files.name’
pipeline.supportingMaps: no visible binding for global variable
‘som.result’
pipeline.supportingMaps: no visible binding for global variable
‘preferences’
pipeline.supportingMaps: no visible global function definition for
‘colramp’
pipeline.supportingMaps: no visible binding for global variable
‘metadata’
pipeline.supportingMaps: no visible binding for global variable ‘p.m’
pipeline.supportingMaps : <anonymous>: no visible binding for global
variable ‘indata’
pipeline.supportingMaps: no visible binding for global variable
‘som.nodes’
pipeline.supportingMaps: no visible binding for global variable
‘indata’
pipeline.supportingMaps : <anonymous>: no visible binding for global
variable ‘metadata’
pipeline.supportingMaps : <anonymous>: no visible binding for global
variable ‘preferences’
pipeline.topologyProfiles: no visible binding for global variable
‘metadata’
pipeline.topologyProfiles: no visible binding for global variable
‘loglog.metadata’
pipeline.topologyProfiles: no visible binding for global variable
‘files.name’
pipeline.topologyProfiles: no visible binding for global variable
‘group.labels’
pipeline.topologyProfiles: no visible binding for global variable
‘spot.list.samples’
pipeline.topologyProfiles: no visible binding for global variable
‘group.colors’
pipeline.topologyProfiles: no visible binding for global variable
‘indata’
pipeline.topologyProfiles: no visible binding for global variable
‘groupwise.group.colors’
pipeline.topologyProfiles : <anonymous>: no visible binding for global
variable ‘group.labels’
pipeline.topologyProfiles: no visible binding for global variable
‘preferences’
pipeline.topologyProfiles : <anonymous>: no visible binding for global
variable ‘preferences’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [16s/23s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
oposSOM-package 9.391 0.048 11.811
opossom.run 3.556 0.016 8.154
* 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 WARNING, 2 NOTEs
See
‘/home/biocbuild/bbs-3.1-bioc/meat/oposSOM.Rcheck/00check.log’
for details.
* installing *source* package ‘oposSOM’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import by ‘igraph::normalize’ when loading ‘oposSOM’
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by ‘igraph::normalize’ when loading ‘oposSOM’
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (oposSOM)