| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:12:48 -0400 (Wed, 15 Apr 2020).
| Package 869/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| IsoformSwitchAnalyzeR 1.8.0 Kristoffer Vitting-Seerup
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] |  | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: IsoformSwitchAnalyzeR |
| Version: 1.8.0 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:IsoformSwitchAnalyzeR.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings IsoformSwitchAnalyzeR_1.8.0.tar.gz |
| StartedAt: 2020-04-15 04:53:44 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 05:04:36 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 651.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: IsoformSwitchAnalyzeR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:IsoformSwitchAnalyzeR.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings IsoformSwitchAnalyzeR_1.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/IsoformSwitchAnalyzeR.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.8.0’
* 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 or elapsed time > 5s
user system elapsed
IsoformSwitchTestDEXSeq 54.888 0.264 59.539
importCufflinksGalaxyData 40.624 0.060 42.460
isoformSwitchAnalysisCombined 22.316 0.084 22.508
extractSequence 16.512 0.020 17.331
analyzeORF 14.992 0.040 15.082
isoformSwitchAnalysisPart1 14.224 0.036 14.411
extractTopSwitches 13.844 0.016 14.857
extractSwitchSummary 12.828 0.028 13.304
analyzeAlternativSplicing 11.648 0.008 12.723
IsoformSwitchTestDRIMSeq 9.252 0.092 10.224
isoformSwitchAnalysisPart2 9.316 0.000 9.422
* 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
‘/home/biocbuild/bbs-3.10-bioc/meat/IsoformSwitchAnalyzeR.Rcheck/00check.log’
for details.
IsoformSwitchAnalyzeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL IsoformSwitchAnalyzeR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’ * installing *source* package ‘IsoformSwitchAnalyzeR’ ... ** using staged installation ** libs gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c utils.c -o utils.o gcc -shared -L/home/biocbuild/bbs-3.10-bioc/R/lib -L/usr/local/lib -o IsoformSwitchAnalyzeR.so utils.o -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.10-bioc/R/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 | 54.888 | 0.264 | 59.539 | |
| IsoformSwitchTestDRIMSeq | 9.252 | 0.092 | 10.224 | |
| analyzeAlternativSplicing | 11.648 | 0.008 | 12.723 | |
| analyzeCPAT | 0.076 | 0.004 | 0.096 | |
| analyzeCPC2 | 0.072 | 0.000 | 0.075 | |
| analyzeIUPred2A | 3.212 | 0.024 | 3.327 | |
| analyzeORF | 14.992 | 0.040 | 15.082 | |
| analyzePFAM | 0.840 | 0.000 | 0.854 | |
| analyzeSignalP | 0.140 | 0.000 | 0.148 | |
| analyzeSwitchConsequences | 1.596 | 0.004 | 1.705 | |
| expressionAnalysisPlots | 1.604 | 0.000 | 1.742 | |
| extractConsequenceEnrichment | 0.908 | 0.012 | 0.967 | |
| extractConsequenceEnrichmentComparison | 2.256 | 0.004 | 2.355 | |
| extractConsequenceSummary | 1.292 | 0.004 | 1.307 | |
| extractGenomeWideAnalysis | 4.180 | 0.040 | 4.578 | |
| extractGenomeWideSplicingAnalysis | 3.744 | 0.004 | 4.093 | |
| extractSequence | 16.512 | 0.020 | 17.331 | |
| extractSplicingEnrichment | 2.148 | 0.000 | 2.257 | |
| extractSplicingEnrichmentComparison | 2.608 | 0.008 | 2.759 | |
| extractSplicingSummary | 1.924 | 0.008 | 2.136 | |
| extractSwitchOverlap | 0.580 | 0.000 | 0.673 | |
| extractSwitchSummary | 12.828 | 0.028 | 13.304 | |
| extractTopSwitches | 13.844 | 0.016 | 14.857 | |
| getCDS | 0 | 0 | 0 | |
| importCufflinksGalaxyData | 40.624 | 0.060 | 42.460 | |
| importGTF | 0.524 | 0.004 | 0.530 | |
| importIsoformExpression | 0.632 | 0.008 | 0.643 | |
| importRdata | 1.132 | 0.004 | 1.225 | |
| isoformSwitchAnalysisCombined | 22.316 | 0.084 | 22.508 | |
| isoformSwitchAnalysisPart1 | 14.224 | 0.036 | 14.411 | |
| isoformSwitchAnalysisPart2 | 9.316 | 0.000 | 9.422 | |
| isoformToGeneExp | 1.596 | 0.012 | 1.625 | |
| isoformToIsoformFraction | 0.228 | 0.000 | 0.228 | |
| preFilter | 0.044 | 0.000 | 0.044 | |
| subsetSwitchAnalyzeRlist | 0.040 | 0.004 | 0.043 | |
| switchAnalyzeRlist | 1.076 | 0.004 | 1.087 | |
| switchPlot | 4.560 | 0.008 | 4.621 | |
| switchPlotTranscript | 2.384 | 0.000 | 2.397 | |
| testData | 0.040 | 0.000 | 0.041 | |