| Back to Multiple platform build/check report for BioC 3.7 |
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This page was generated on 2018-10-17 08:30:20 -0400 (Wed, 17 Oct 2018).
| Package 755/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| IsoformSwitchAnalyzeR 1.2.0 Kristoffer Vitting-Seerup
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] |  | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: IsoformSwitchAnalyzeR |
| Version: 1.2.0 |
| Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:IsoformSwitchAnalyzeR.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings IsoformSwitchAnalyzeR_1.2.0.tar.gz |
| StartedAt: 2018-10-16 01:23:57 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 01:29:29 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 331.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: IsoformSwitchAnalyzeR.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:IsoformSwitchAnalyzeR.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings IsoformSwitchAnalyzeR_1.2.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/IsoformSwitchAnalyzeR.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.2.0’
* 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 ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
createSwitchAnalyzeRlist: no visible global function definition for
'Rle'
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 : <anonymous> : <anonymous>: no
visible global function definition for 'fisher.test'
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 : <anonymous> : <anonymous>: no
visible global function definition for 'fisher.test'
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'
extractSwitchOverlap: no visible global function definition for
'plotViewport'
extractSwitchOverlap: no visible global function definition for
'grid.draw'
extractSwitchOverlap: no visible global function definition for
'popViewport'
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 Rle
Significant feature2 fisher.test geneFraction gene_expression
grid.draw idNr isoFraction isoform_feature nrGenesWithConsequences
nrIsoWithConsequences plotViewport popViewport propCiHi propCiLo
propOfRelevantEvents propUp propUpCiHi propUpCiLo queryHits sigEval
sigLevel sigLevelPos significance splicingResult switchConsequence
value variable x xmax xmin y yend ymax ymin
Consider adding
importFrom("stats", "fisher.test")
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 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
isoformSwitchAnalysisCombined 15.364 0.128 15.505
IsoformSwitchTestDRIMSeq 9.372 0.112 9.869
isoformSwitchAnalysisPart1 9.260 0.156 9.425
analyzeAlternativSplicing 6.772 0.008 6.786
* 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-3.7-bioc/meat/IsoformSwitchAnalyzeR.Rcheck/00check.log’
for details.
IsoformSwitchAnalyzeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL IsoformSwitchAnalyzeR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’ * installing *source* package ‘IsoformSwitchAnalyzeR’ ... ** libs gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c utils.c -o utils.o gcc -shared -L/home/biocbuild/bbs-3.7-bioc/R/lib -L/usr/local/lib -o IsoformSwitchAnalyzeR.so utils.o -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.7-bioc/R/library/IsoformSwitchAnalyzeR/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import 'plyr::desc' by 'IRanges::desc' when loading 'IsoformSwitchAnalyzeR' Warning: replacing previous import 'plyr::count' by 'cummeRbund::count' when loading 'IsoformSwitchAnalyzeR' Warning: replacing previous import 'GenomicRanges::promoters' by 'cummeRbund::promoters' when loading 'IsoformSwitchAnalyzeR' Warning: replacing previous import 'cummeRbund::samples' by 'DRIMSeq::samples' when loading 'IsoformSwitchAnalyzeR' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded Warning: replacing previous import 'plyr::desc' by 'IRanges::desc' when loading 'IsoformSwitchAnalyzeR' Warning: replacing previous import 'plyr::count' by 'cummeRbund::count' when loading 'IsoformSwitchAnalyzeR' Warning: replacing previous import 'GenomicRanges::promoters' by 'cummeRbund::promoters' when loading 'IsoformSwitchAnalyzeR' Warning: replacing previous import 'cummeRbund::samples' by 'DRIMSeq::samples' when loading 'IsoformSwitchAnalyzeR' * DONE (IsoformSwitchAnalyzeR)
IsoformSwitchAnalyzeR.Rcheck/IsoformSwitchAnalyzeR-Ex.timings
| name | user | system | elapsed | |
| IsoformSwitchTestDRIMSeq | 9.372 | 0.112 | 9.869 | |
| analyzeAlternativSplicing | 6.772 | 0.008 | 6.786 | |
| analyzeCPAT | 0.036 | 0.000 | 0.048 | |
| analyzeORF | 0.440 | 0.004 | 0.443 | |
| analyzePFAM | 0.504 | 0.004 | 0.510 | |
| analyzeSignalP | 0.072 | 0.000 | 0.089 | |
| analyzeSwitchConsequences | 0.912 | 0.004 | 0.920 | |
| expressionAnalysisPlots | 1.224 | 0.004 | 1.230 | |
| extractCallibarionStatus | 0.040 | 0.000 | 0.037 | |
| extractConsequenceEnrichment | 0.500 | 0.000 | 0.502 | |
| extractConsequenceEnrichmentComparison | 0.816 | 0.004 | 0.823 | |
| extractConsequenceSummary | 0.780 | 0.000 | 0.781 | |
| extractExpressionMatrix | 0.208 | 0.004 | 0.211 | |
| extractGenomeWideAnalysis | 2.448 | 0.016 | 2.466 | |
| extractGenomeWideSplicingAnalysis | 2.488 | 0.000 | 2.494 | |
| extractSequence | 0.656 | 0.004 | 0.662 | |
| extractSplicingEnrichment | 1.264 | 0.016 | 1.282 | |
| extractSplicingEnrichmentComparison | 1.340 | 0.000 | 1.341 | |
| extractSplicingSummary | 1.244 | 0.000 | 1.247 | |
| extractSwitchOverlap | 0.332 | 0.008 | 0.353 | |
| extractSwitchSummary | 0.040 | 0.000 | 0.042 | |
| extractTopSwitches | 0.172 | 0.000 | 0.170 | |
| getCDS | 0.000 | 0.000 | 0.001 | |
| importCufflinksData | 3.984 | 0.032 | 4.022 | |
| importCufflinksGalaxyData | 1.824 | 0.000 | 1.827 | |
| importGTF | 0.640 | 0.004 | 0.645 | |
| importRdata | 3.556 | 0.032 | 3.593 | |
| isoformSwitchAnalysisCombined | 15.364 | 0.128 | 15.505 | |
| isoformSwitchAnalysisPart1 | 9.260 | 0.156 | 9.425 | |
| isoformSwitchAnalysisPart2 | 3.432 | 0.028 | 3.461 | |
| isoformSwitchTest | 0.036 | 0.004 | 0.040 | |
| isoformToGeneExp | 1.728 | 0.024 | 1.751 | |
| preFilter | 0.020 | 0.000 | 0.019 | |
| prepareCuffExample | 1.656 | 0.020 | 1.676 | |
| switchAnalyzeRlist | 3.288 | 0.024 | 3.314 | |
| switchPlot | 2.184 | 0.000 | 2.186 | |
| switchPlotTranscript | 0.72 | 0.00 | 0.72 | |
| testData | 0.016 | 0.000 | 0.014 | |