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CHECK report for IsoformSwitchAnalyzeR on merida1

This page was generated on 2020-10-24 11:08:54 -0400 (Sat, 24 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE IsoformSwitchAnalyzeR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 920/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IsoformSwitchAnalyzeR 1.11.11
Kristoffer Vitting-Seerup
Snapshot Date: 2020-10-23 14:40:36 -0400 (Fri, 23 Oct 2020)
URL: https://git.bioconductor.org/packages/IsoformSwitchAnalyzeR
Branch: master
Last Commit: 83fbe04
Last Changed Date: 2020-10-13 08:25:03 -0400 (Tue, 13 Oct 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK  OK  OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: IsoformSwitchAnalyzeR
Version: 1.11.11
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_1.11.11.tar.gz
StartedAt: 2020-10-24 02:57:31 -0400 (Sat, 24 Oct 2020)
EndedAt: 2020-10-24 03:12:25 -0400 (Sat, 24 Oct 2020)
EllapsedTime: 894.8 seconds
RetCode: 0
Status:  OK 
CheckDir: IsoformSwitchAnalyzeR.Rcheck
Warnings: 0

Command output

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###
### 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_1.11.11.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/IsoformSwitchAnalyzeR.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.11.11’
* 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 ... NOTE
  installed size is  6.3Mb
  sub-directories of 1Mb or more:
    extdata   4.2Mb
* 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'
createSwitchAnalyzeRlist: no visible global function definition for
  'package.version'
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
  'AStype'
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'
importGTF: no visible binding for global variable 'gene_id'
importGTF: no visible binding for global variable 'gene_name'
importRdata: no visible binding for global variable 'isoform_id'
importRdata: no visible binding for global variable 'gene_id'
importRdata: no visible binding for global variable 'gene_name'
importRdata: no visible binding for global variable 'n_gene_names'
importRdata: no visible binding for global variable 'n_iso_na'
importRdata: no visible global function definition for 'queryHits'
importRdata: no visible global function definition for 'subjectHits'
importRdata: no visible binding for global variable 'novel_iso'
importRdata: no visible binding for global variable 'known_gene_name'
importRdata: no visible binding for global variable 'nt_overlap'
importRdata: no visible binding for global variable 'frac_overlap'
importRdata: no visible binding for global variable
  'log2_overlap_ratio'
importRdata: no visible binding for global variable 'has_gene_name'
importRdata: no visible binding for global variable 'has_novel_iso'
importSalmonData: no visible global function definition for 'metadata'
importSalmonData: no visible global function definition for 'assay'
isoformToGeneExp: no visible binding for global variable 'gene_id'
isoformToGeneExp: no visible binding for global variable 'gene_name'
isoformToGeneExp: no visible binding for global variable 'isoform_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:
  AStype CI_down CI_hi CI_low CI_up Comparison Condition Domain IF
  Significant assay feature2 frac_overlap geneFraction gene_expression
  gene_id gene_name has_gene_name has_novel_iso idNr isoFraction
  isoform_feature isoform_id known_gene_name log2_overlap_ratio
  metadata nTot n_gene_names n_iso_na novel_iso nrGenesWithConsequences
  nrIsoWithConsequences nt_overlap package.version 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
importSalmonData              55.728  3.173  73.870
IsoformSwitchTestDEXSeq       55.985  0.521  56.608
importCufflinksGalaxyData     41.616  0.315  41.995
IsoformSwitchTestDRIMSeq      31.757  0.127  31.922
isoformSwitchAnalysisCombined 20.736  0.372  21.140
prepareSalmonFilesDataFrame   19.526  0.393  24.566
extractSequence               16.965  0.081  17.066
extractTopSwitches            15.481  0.074  15.573
isoformSwitchAnalysisPart1    15.144  0.089  15.252
extractSwitchSummary          14.651  0.070  14.738
analyzeORF                    14.607  0.100  14.726
analyzeAlternativSplicing     12.310  0.038  12.363
isoformSwitchAnalysisPart2     9.721  0.161   9.896
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/IsoformSwitchAnalyzeR.Rcheck/00check.log’
for details.



Installation output

IsoformSwitchAnalyzeR.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL IsoformSwitchAnalyzeR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘IsoformSwitchAnalyzeR’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c utils.c -o utils.o
clang -mmacosx-version-min=10.13 -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)

Tests output


Example timings

IsoformSwitchAnalyzeR.Rcheck/IsoformSwitchAnalyzeR-Ex.timings

nameusersystemelapsed
IsoformSwitchTestDEXSeq55.985 0.52156.608
IsoformSwitchTestDRIMSeq31.757 0.12731.922
analyzeAlternativSplicing12.310 0.03812.363
analyzeCPAT0.0920.0050.097
analyzeCPC20.0750.0030.079
analyzeIUPred2A3.5600.0353.600
analyzeORF14.607 0.10014.726
analyzePFAM0.8970.0100.907
analyzeSignalP0.1600.0060.167
analyzeSwitchConsequences1.5170.0201.538
expressionAnalysisPlots1.4710.0131.487
extractConsequenceEnrichment0.7770.0100.788
extractConsequenceEnrichmentComparison1.2500.0091.261
extractConsequenceSummary1.2670.0071.276
extractGeneExpression0.0860.0040.090
extractGenomeWideAnalysis4.1020.0754.182
extractGenomeWideSplicingAnalysis3.8280.0633.897
extractSequence16.965 0.08117.066
extractSplicingEnrichment1.8930.0171.911
extractSplicingEnrichmentComparison2.1910.0102.204
extractSplicingSummary1.6310.0081.641
extractSwitchOverlap0.5980.0120.612
extractSwitchSummary14.651 0.07014.738
extractTopSwitches15.481 0.07415.573
getCDS0.0000.0000.001
importCufflinksGalaxyData41.616 0.31541.995
importGTF1.3310.0051.336
importIsoformExpression0.8620.0270.899
importRdata2.2700.0272.301
importSalmonData55.728 3.17373.870
isoformSwitchAnalysisCombined20.736 0.37221.140
isoformSwitchAnalysisPart115.144 0.08915.252
isoformSwitchAnalysisPart29.7210.1619.896
isoformToGeneExp3.3160.0483.371
isoformToIsoformFraction0.3370.0130.350
preFilter0.0360.0040.041
prepareSalmonFilesDataFrame19.526 0.39324.566
subsetSwitchAnalyzeRlist0.0320.0040.036
switchAnalyzeRlist2.1990.0282.231
switchPlot4.9100.0204.948
switchPlotTranscript3.5940.0663.722
testData0.0300.0040.033