| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:48:10 -0500 (Thu, 16 Jan 2020).
| Package 866/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| IsoformSwitchAnalyzeR 1.9.0 Kristoffer Vitting-Seerup
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: IsoformSwitchAnalyzeR |
| Version: 1.9.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:IsoformSwitchAnalyzeR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings IsoformSwitchAnalyzeR_1.9.0.tar.gz |
| StartedAt: 2020-01-16 05:43:59 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 05:57:56 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 837.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: IsoformSwitchAnalyzeR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:IsoformSwitchAnalyzeR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings IsoformSwitchAnalyzeR_1.9.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/IsoformSwitchAnalyzeR.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.9.0’
* 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 ... NOTE
Malformed Title field: should not end in a period.
* 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
analyzeIUPred2A: no visible global function definition for ‘queryHits’
analyzeIUPred2A: no visible global function definition for
‘subjectHits’
compareAnnotationOfTwoIsoforms: no visible global function definition
for ‘queryHits’
compareAnnotationOfTwoIsoforms: no visible global function definition
for ‘subjectHits’
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’
extractConsequenceEnrichment: no visible binding for global variable
‘nTot’
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 ‘nTot’
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
‘AStype2’
extractSplicingEnrichment: no visible binding for global variable
‘propUp’
extractSplicingEnrichment: no visible binding for global variable
‘Significant’
extractSplicingEnrichment: no visible binding for global variable
‘nTot’
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 ‘nTot’
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’
grangesFracOverlap: no visible global function definition for
‘queryHits’
grangesFracOverlap: no visible global function definition for
‘subjectHits’
isoformToGeneExp: no visible binding for global variable ‘isoform_id’
isoformToGeneExp: no visible binding for global variable ‘gene_id’
preFilter: no visible global function definition for ‘setdff’
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:
AStype2 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 nTot nrGenesWithConsequences
nrIsoWithConsequences propCiHi propCiLo propOfRelevantEvents propUp
propUpCiHi propUpCiLo queryHits setdff sigEval sigLevel sigLevelPos
significance splicingResult subjectHits 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 (user + system) or elapsed time > 5s
user system elapsed
IsoformSwitchTestDEXSeq 66.944 1.590 68.997
importCufflinksGalaxyData 46.639 0.710 47.378
isoformSwitchAnalysisCombined 25.641 0.781 26.424
extractSequence 21.466 0.264 21.737
analyzeORF 21.333 0.124 21.475
extractSwitchSummary 18.120 0.115 18.239
isoformSwitchAnalysisPart1 17.928 0.148 18.076
extractTopSwitches 17.820 0.113 17.936
IsoformSwitchTestDRIMSeq 16.862 0.266 17.613
analyzeAlternativSplicing 15.585 0.039 15.651
isoformSwitchAnalysisPart2 12.386 0.464 12.852
switchPlot 6.393 0.051 6.444
extractGenomeWideSplicingAnalysis 5.048 0.255 5.398
extractGenomeWideAnalysis 5.030 0.171 5.235
* 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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.11-bioc/meat/IsoformSwitchAnalyzeR.Rcheck/00check.log’
for details.
IsoformSwitchAnalyzeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL IsoformSwitchAnalyzeR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘IsoformSwitchAnalyzeR’ ... ** using staged installation ** libs clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c utils.c -o utils.o clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o IsoformSwitchAnalyzeR.so utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-IsoformSwitchAnalyzeR/00new/IsoformSwitchAnalyzeR/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (IsoformSwitchAnalyzeR)
IsoformSwitchAnalyzeR.Rcheck/IsoformSwitchAnalyzeR-Ex.timings
| name | user | system | elapsed | |
| IsoformSwitchTestDEXSeq | 66.944 | 1.590 | 68.997 | |
| IsoformSwitchTestDRIMSeq | 16.862 | 0.266 | 17.613 | |
| analyzeAlternativSplicing | 15.585 | 0.039 | 15.651 | |
| analyzeCPAT | 0.088 | 0.011 | 0.101 | |
| analyzeCPC2 | 0.069 | 0.007 | 0.077 | |
| analyzeIUPred2A | 4.385 | 0.103 | 4.492 | |
| analyzeORF | 21.333 | 0.124 | 21.475 | |
| analyzePFAM | 1.042 | 0.012 | 1.056 | |
| analyzeSignalP | 0.147 | 0.010 | 0.157 | |
| analyzeSwitchConsequences | 1.932 | 0.027 | 1.964 | |
| expressionAnalysisPlots | 2.207 | 0.017 | 2.228 | |
| extractConsequenceEnrichment | 1.254 | 0.017 | 1.277 | |
| extractConsequenceEnrichmentComparison | 1.728 | 0.017 | 1.748 | |
| extractConsequenceSummary | 1.411 | 0.020 | 1.442 | |
| extractGenomeWideAnalysis | 5.030 | 0.171 | 5.235 | |
| extractGenomeWideSplicingAnalysis | 5.048 | 0.255 | 5.398 | |
| extractSequence | 21.466 | 0.264 | 21.737 | |
| extractSplicingEnrichment | 2.740 | 0.050 | 2.791 | |
| extractSplicingEnrichmentComparison | 2.793 | 0.029 | 2.824 | |
| extractSplicingSummary | 3.016 | 0.022 | 3.041 | |
| extractSwitchOverlap | 0.582 | 0.022 | 0.606 | |
| extractSwitchSummary | 18.120 | 0.115 | 18.239 | |
| extractTopSwitches | 17.820 | 0.113 | 17.936 | |
| getCDS | 0 | 0 | 0 | |
| importCufflinksGalaxyData | 46.639 | 0.710 | 47.378 | |
| importGTF | 0.656 | 0.004 | 0.660 | |
| importIsoformExpression | 0.687 | 0.021 | 0.709 | |
| importRdata | 1.573 | 0.041 | 1.616 | |
| isoformSwitchAnalysisCombined | 25.641 | 0.781 | 26.424 | |
| isoformSwitchAnalysisPart1 | 17.928 | 0.148 | 18.076 | |
| isoformSwitchAnalysisPart2 | 12.386 | 0.464 | 12.852 | |
| isoformToGeneExp | 2.271 | 0.126 | 2.398 | |
| isoformToIsoformFraction | 0.229 | 0.013 | 0.242 | |
| preFilter | 0.051 | 0.008 | 0.059 | |
| subsetSwitchAnalyzeRlist | 0.062 | 0.012 | 0.073 | |
| switchAnalyzeRlist | 1.403 | 0.055 | 1.461 | |
| switchPlot | 6.393 | 0.051 | 6.444 | |
| switchPlotTranscript | 3.448 | 0.024 | 3.474 | |
| testData | 0.040 | 0.008 | 0.048 | |