| Back to Multiple platform build/check report for BioC 3.7 |
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This page was generated on 2018-10-17 08:58:20 -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: /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_1.2.0.tar.gz |
| StartedAt: 2018-10-16 22:09:46 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 22:17:23 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 456.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: IsoformSwitchAnalyzeR.Rcheck |
| Warnings: 0 |
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### Running command:
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### /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_1.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/IsoformSwitchAnalyzeR.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.2.0’
* 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 21.366 0.211 21.687
isoformSwitchAnalysisPart1 14.369 0.122 14.593
IsoformSwitchTestDRIMSeq 13.820 0.299 14.252
analyzeAlternativSplicing 10.260 0.036 10.582
importCufflinksData 6.702 0.127 6.883
importRdata 5.481 0.109 5.657
isoformSwitchAnalysisPart2 5.032 0.141 5.183
* 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
‘/Users/biocbuild/bbs-3.7-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/3.5/Resources/library’ * installing *source* package ‘IsoformSwitchAnalyzeR’ ... ** libs clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -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/3.5/Resources/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 | 13.820 | 0.299 | 14.252 | |
| analyzeAlternativSplicing | 10.260 | 0.036 | 10.582 | |
| analyzeCPAT | 0.045 | 0.007 | 0.053 | |
| analyzeORF | 0.633 | 0.018 | 0.656 | |
| analyzePFAM | 0.847 | 0.009 | 0.864 | |
| analyzeSignalP | 0.103 | 0.007 | 0.112 | |
| analyzeSwitchConsequences | 1.359 | 0.023 | 1.393 | |
| expressionAnalysisPlots | 1.752 | 0.016 | 1.785 | |
| extractCallibarionStatus | 0.057 | 0.011 | 0.068 | |
| extractConsequenceEnrichment | 0.721 | 0.010 | 0.738 | |
| extractConsequenceEnrichmentComparison | 1.114 | 0.013 | 1.146 | |
| extractConsequenceSummary | 1.032 | 0.013 | 1.056 | |
| extractExpressionMatrix | 0.288 | 0.011 | 0.303 | |
| extractGenomeWideAnalysis | 3.437 | 0.095 | 3.558 | |
| extractGenomeWideSplicingAnalysis | 3.571 | 0.100 | 3.690 | |
| extractSequence | 0.787 | 0.011 | 0.798 | |
| extractSplicingEnrichment | 1.753 | 0.020 | 1.780 | |
| extractSplicingEnrichmentComparison | 1.976 | 0.027 | 2.008 | |
| extractSplicingSummary | 1.747 | 0.011 | 1.766 | |
| extractSwitchOverlap | 0.448 | 0.017 | 0.469 | |
| extractSwitchSummary | 0.056 | 0.006 | 0.061 | |
| extractTopSwitches | 0.184 | 0.013 | 0.199 | |
| getCDS | 0.001 | 0.000 | 0.001 | |
| importCufflinksData | 6.702 | 0.127 | 6.883 | |
| importCufflinksGalaxyData | 2.888 | 0.010 | 2.908 | |
| importGTF | 0.971 | 0.006 | 0.979 | |
| importRdata | 5.481 | 0.109 | 5.657 | |
| isoformSwitchAnalysisCombined | 21.366 | 0.211 | 21.687 | |
| isoformSwitchAnalysisPart1 | 14.369 | 0.122 | 14.593 | |
| isoformSwitchAnalysisPart2 | 5.032 | 0.141 | 5.183 | |
| isoformSwitchTest | 0.048 | 0.003 | 0.051 | |
| isoformToGeneExp | 2.717 | 0.104 | 2.869 | |
| preFilter | 0.019 | 0.002 | 0.021 | |
| prepareCuffExample | 2.648 | 0.099 | 2.785 | |
| switchAnalyzeRlist | 4.441 | 0.117 | 4.595 | |
| switchPlot | 2.614 | 0.015 | 2.634 | |
| switchPlotTranscript | 0.880 | 0.008 | 0.897 | |
| testData | 0.016 | 0.004 | 0.020 | |