| Back to Multiple platform build/check report for BioC 3.8 |
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This page was generated on 2019-04-16 11:52:50 -0400 (Tue, 16 Apr 2019).
| Package 799/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| IsoformSwitchAnalyzeR 1.4.0 Kristoffer Vitting-Seerup
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ WARNINGS ] |  | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: IsoformSwitchAnalyzeR |
| Version: 1.4.0 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:IsoformSwitchAnalyzeR.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings IsoformSwitchAnalyzeR_1.4.0.tar.gz |
| StartedAt: 2019-04-16 00:54:13 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 01:01:19 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 426.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: IsoformSwitchAnalyzeR.Rcheck |
| Warnings: 1 |
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### Running command:
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### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:IsoformSwitchAnalyzeR.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings IsoformSwitchAnalyzeR_1.4.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/IsoformSwitchAnalyzeR.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IsoformSwitchAnalyzeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘IsoformSwitchAnalyzeR’ 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 ‘IsoformSwitchAnalyzeR’ can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import ‘DEXSeq::plotMA’ by ‘limma::plotMA’ when loading ‘IsoformSwitchAnalyzeR’
See ‘/home/biocbuild/bbs-3.8-bioc/meat/IsoformSwitchAnalyzeR.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘limma’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
expressionAnalysisPlot: no visible binding for global variable
‘Condition’
expressionAnalysisPlot: no visible binding for global variable
‘gene_expression’
expressionAnalysisPlot: no visible binding for global variable ‘CI_up’
expressionAnalysisPlot: no visible binding for global variable
‘CI_down’
expressionAnalysisPlot: no visible binding for global variable
‘sigLevelPos’
expressionAnalysisPlot: no visible binding for global variable
‘sigLevel’
expressionAnalysisPlot: no visible binding for global variable ‘CI_hi’
expressionAnalysisPlot: no visible binding for global variable ‘CI_low’
expressionAnalysisPlot: no visible binding for global variable ‘ymax’
expressionAnalysisPlot: no visible binding for global variable
‘sigEval’
expressionAnalysisPlot: no visible binding for global variable ‘idNr’
expressionAnalysisPlot: no visible binding for global variable ‘IF’
extractConsequenceEnrichment: no visible binding for global variable
‘feature2’
extractConsequenceEnrichment: no visible binding for global variable
‘propOfRelevantEvents’
extractConsequenceEnrichment: no visible binding for global variable
‘Significant’
extractConsequenceEnrichment: no visible binding for global variable
‘propCiLo’
extractConsequenceEnrichment: no visible binding for global variable
‘propCiHi’
extractConsequenceEnrichmentComparison: no visible binding for global
variable ‘Comparison’
extractConsequenceEnrichmentComparison: no visible binding for global
variable ‘propOfRelevantEvents’
extractConsequenceEnrichmentComparison: no visible binding for global
variable ‘Significant’
extractConsequenceEnrichmentComparison: no visible binding for global
variable ‘propCiHi’
extractConsequenceEnrichmentComparison: no visible binding for global
variable ‘propCiLo’
extractConsequenceGenomeWide: no visible binding for global variable
‘isoform_feature’
extractConsequenceGenomeWide: no visible binding for global variable
‘value’
extractConsequenceGenomeWide: no visible binding for global variable
‘variable’
extractConsequenceGenomeWide: no visible binding for global variable
‘ymax’
extractConsequenceGenomeWide: no visible binding for global variable
‘significance’
extractConsequenceGenomeWide: no visible binding for global variable
‘idNr’
extractConsequenceSummary: no visible binding for global variable
‘switchConsequence’
extractConsequenceSummary: no visible binding for global variable
‘geneFraction’
extractConsequenceSummary: no visible binding for global variable
‘nrGenesWithConsequences’
extractConsequenceSummary: no visible binding for global variable
‘isoFraction’
extractConsequenceSummary: no visible binding for global variable
‘nrIsoWithConsequences’
extractSplicingEnrichment: no visible binding for global variable
‘AStype’
extractSplicingEnrichment: no visible binding for global variable
‘propUp’
extractSplicingEnrichment: no visible binding for global variable
‘Significant’
extractSplicingEnrichment: no visible binding for global variable
‘propUpCiHi’
extractSplicingEnrichment: no visible binding for global variable
‘propUpCiLo’
extractSplicingEnrichmentComparison: no visible binding for global
variable ‘Comparison’
extractSplicingEnrichmentComparison: no visible binding for global
variable ‘propUp’
extractSplicingEnrichmentComparison: no visible binding for global
variable ‘Significant’
extractSplicingEnrichmentComparison: no visible binding for global
variable ‘propUpCiHi’
extractSplicingEnrichmentComparison: no visible binding for global
variable ‘propUpCiLo’
extractSplicingGenomeWide: no visible binding for global variable
‘isoform_feature’
extractSplicingGenomeWide: no visible binding for global variable
‘value’
extractSplicingGenomeWide: no visible binding for global variable
‘variable’
extractSplicingGenomeWide: no visible binding for global variable
‘ymax’
extractSplicingGenomeWide: no visible binding for global variable
‘significance’
extractSplicingGenomeWide: no visible binding for global variable
‘idNr’
extractSplicingSummary: no visible binding for global variable
‘splicingResult’
extractSplicingSummary: no visible binding for global variable
‘geneFraction’
extractSplicingSummary: no visible binding for global variable
‘nrGenesWithConsequences’
extractSplicingSummary: no visible binding for global variable
‘isoFraction’
extractSplicingSummary: no visible binding for global variable
‘nrIsoWithConsequences’
isoformToGeneExp: no visible binding for global variable ‘isoform_id’
isoformToGeneExp: no visible binding for global variable ‘gene_id’
switchPlotTranscript: no visible global function definition for
‘queryHits’
switchPlotTranscript: no visible binding for global variable ‘y’
switchPlotTranscript: no visible binding for global variable ‘yend’
switchPlotTranscript: no visible binding for global variable ‘x’
switchPlotTranscript: no visible binding for global variable ‘ymin’
switchPlotTranscript: no visible binding for global variable ‘xmin’
switchPlotTranscript: no visible binding for global variable ‘ymax’
switchPlotTranscript: no visible binding for global variable ‘xmax’
switchPlotTranscript: no visible binding for global variable ‘Domain’
Undefined global functions or variables:
AStype CI_down CI_hi CI_low CI_up Comparison Condition Domain IF
Significant feature2 geneFraction gene_expression gene_id idNr
isoFraction isoform_feature isoform_id nrGenesWithConsequences
nrIsoWithConsequences propCiHi propCiLo propOfRelevantEvents propUp
propUpCiHi propUpCiLo queryHits sigEval sigLevel sigLevelPos
significance splicingResult switchConsequence value variable x xmax
xmin y yend ymax ymin
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
IsoformSwitchTestDEXSeq 31.264 0.120 31.456
isoformSwitchAnalysisCombined 12.432 0.052 12.499
analyzeAlternativSplicing 9.580 0.000 9.588
IsoformSwitchTestDRIMSeq 9.048 0.036 9.104
extractSequence 9.040 0.012 9.146
analyzeORF 8.168 0.024 8.207
extractTopSwitches 6.596 0.016 6.623
extractSwitchSummary 6.460 0.000 6.468
isoformSwitchAnalysisPart1 5.768 0.016 5.789
* 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, 3 NOTEs
See
‘/home/biocbuild/bbs-3.8-bioc/meat/IsoformSwitchAnalyzeR.Rcheck/00check.log’
for details.
IsoformSwitchAnalyzeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL IsoformSwitchAnalyzeR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’ * installing *source* package ‘IsoformSwitchAnalyzeR’ ... ** libs gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c utils.c -o utils.o gcc -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o IsoformSwitchAnalyzeR.so utils.o -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.8-bioc/R/library/IsoformSwitchAnalyzeR/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import ‘DEXSeq::plotMA’ by ‘limma::plotMA’ when loading ‘IsoformSwitchAnalyzeR’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded Warning: replacing previous import ‘DEXSeq::plotMA’ by ‘limma::plotMA’ when loading ‘IsoformSwitchAnalyzeR’ * DONE (IsoformSwitchAnalyzeR)
IsoformSwitchAnalyzeR.Rcheck/IsoformSwitchAnalyzeR-Ex.timings
| name | user | system | elapsed | |
| IsoformSwitchTestDEXSeq | 31.264 | 0.120 | 31.456 | |
| IsoformSwitchTestDRIMSeq | 9.048 | 0.036 | 9.104 | |
| analyzeAlternativSplicing | 9.580 | 0.000 | 9.588 | |
| analyzeCPAT | 0.064 | 0.000 | 0.080 | |
| analyzeORF | 8.168 | 0.024 | 8.207 | |
| analyzePFAM | 0.728 | 0.004 | 0.761 | |
| analyzeSignalP | 0.068 | 0.000 | 0.078 | |
| analyzeSwitchConsequences | 0.864 | 0.000 | 0.870 | |
| expressionAnalysisPlots | 1.552 | 0.000 | 1.555 | |
| extractConsequenceEnrichment | 0.712 | 0.000 | 0.712 | |
| extractConsequenceEnrichmentComparison | 0.836 | 0.004 | 0.841 | |
| extractConsequenceSummary | 1.128 | 0.004 | 1.137 | |
| extractExpressionMatrix | 0.212 | 0.004 | 0.214 | |
| extractGenomeWideAnalysis | 3.460 | 0.020 | 3.485 | |
| extractGenomeWideSplicingAnalysis | 3.588 | 0.012 | 3.632 | |
| extractSequence | 9.040 | 0.012 | 9.146 | |
| extractSplicingEnrichment | 1.708 | 0.000 | 1.719 | |
| extractSplicingEnrichmentComparison | 1.688 | 0.000 | 1.691 | |
| extractSplicingSummary | 1.384 | 0.004 | 1.388 | |
| extractSwitchOverlap | 0.356 | 0.004 | 0.372 | |
| extractSwitchSummary | 6.460 | 0.000 | 6.468 | |
| extractTopSwitches | 6.596 | 0.016 | 6.623 | |
| getCDS | 0.000 | 0.000 | 0.001 | |
| importCufflinksGalaxyData | 1.260 | 0.008 | 1.330 | |
| importGTF | 0.324 | 0.000 | 0.326 | |
| importIsoformExpression | 0.044 | 0.004 | 0.044 | |
| importRdata | 1.184 | 0.004 | 1.190 | |
| isoformSwitchAnalysisCombined | 12.432 | 0.052 | 12.499 | |
| isoformSwitchAnalysisPart1 | 5.768 | 0.016 | 5.789 | |
| isoformSwitchAnalysisPart2 | 3.808 | 0.012 | 3.822 | |
| isoformToGeneExp | 0.128 | 0.000 | 0.129 | |
| isoformToIsoformFraction | 0.128 | 0.000 | 0.129 | |
| preFilter | 0.020 | 0.000 | 0.019 | |
| removeAnnoationData | 0.868 | 0.000 | 0.867 | |
| subsetSwitchAnalyzeRlist | 0.020 | 0.000 | 0.019 | |
| switchAnalyzeRlist | 0.820 | 0.004 | 0.825 | |
| switchPlot | 3.008 | 0.008 | 3.020 | |
| switchPlotTranscript | 0.976 | 0.008 | 0.991 | |
| testData | 0.012 | 0.004 | 0.015 | |