Package: IsoformSwitchAnalyzeR

Version: 1.4.0

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_1.4.0.tar.gz

StartedAt: 2019-04-16 00:47:16 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 00:54:37 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 441.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: IsoformSwitchAnalyzeR.Rcheck

Warnings: 1

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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_1.4.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/IsoformSwitchAnalyzeR.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.4.0’
* 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 ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘DEXSeq::plotMA’ by ‘limma::plotMA’ when loading ‘IsoformSwitchAnalyzeR’
See ‘/Users/biocbuild/bbs-3.8-bioc/meat/IsoformSwitchAnalyzeR.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘limma’
A package should be listed in only one of these fields.
* 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
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: 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: 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’
isoformToGeneExp: no visible binding for global variable ‘isoform_id’
isoformToGeneExp: no visible binding for global variable ‘gene_id’
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 feature2 geneFraction gene_expression gene_id idNr
  isoFraction isoform_feature isoform_id nrGenesWithConsequences
  nrIsoWithConsequences propCiHi propCiLo propOfRelevantEvents propUp
  propUpCiHi propUpCiLo queryHits sigEval sigLevel sigLevelPos
  significance splicingResult 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       27.589  0.379  28.066
isoformSwitchAnalysisCombined 14.366  0.275  14.713
analyzeAlternativSplicing      9.893  0.027   9.995
IsoformSwitchTestDRIMSeq       8.606  0.068   8.721
extractSequence                8.614  0.049   8.720
analyzeORF                     8.362  0.044   8.451
isoformSwitchAnalysisPart1     7.877  0.053   7.958
extractSwitchSummary           5.462  0.027   5.515
extractTopSwitches             5.411  0.031   5.453
isoformSwitchAnalysisPart2     5.284  0.140   5.439
* 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: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/IsoformSwitchAnalyzeR.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL IsoformSwitchAnalyzeR
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* 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 ‘DEXSeq::plotMA’ by ‘limma::plotMA’ when loading ‘IsoformSwitchAnalyzeR’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘DEXSeq::plotMA’ by ‘limma::plotMA’ when loading ‘IsoformSwitchAnalyzeR’
* DONE (IsoformSwitchAnalyzeR)

name	user	system	elapsed
IsoformSwitchTestDEXSeq	27.589	0.379	28.066
IsoformSwitchTestDRIMSeq	8.606	0.068	8.721
analyzeAlternativSplicing	9.893	0.027	9.995
analyzeCPAT	0.054	0.006	0.061
analyzeORF	8.362	0.044	8.451
analyzePFAM	0.762	0.009	0.776
analyzeSignalP	0.102	0.006	0.109
analyzeSwitchConsequences	1.089	0.015	1.111
expressionAnalysisPlots	1.394	0.011	1.409
extractConsequenceEnrichment	0.613	0.006	0.625
extractConsequenceEnrichmentComparison	1.125	0.010	1.169
extractConsequenceSummary	0.945	0.010	0.957
extractExpressionMatrix	0.293	0.010	0.327
extractGenomeWideAnalysis	3.911	0.088	4.450
extractGenomeWideSplicingAnalysis	3.324	0.078	3.468
extractSequence	8.614	0.049	8.720
extractSplicingEnrichment	1.733	0.020	1.765
extractSplicingEnrichmentComparison	1.870	0.028	1.904
extractSplicingSummary	2.216	0.022	2.242
extractSwitchOverlap	0.445	0.016	0.466
extractSwitchSummary	5.462	0.027	5.515
extractTopSwitches	5.411	0.031	5.453
getCDS	0	0	0
importCufflinksGalaxyData	0.957	0.014	0.978
importGTF	0.252	0.003	0.255
importIsoformExpression	0.754	0.006	0.762
importRdata	0.823	0.007	0.830
isoformSwitchAnalysisCombined	14.366	0.275	14.713
isoformSwitchAnalysisPart1	7.877	0.053	7.958
isoformSwitchAnalysisPart2	5.284	0.140	5.439
isoformToGeneExp	0.142	0.005	0.147
isoformToIsoformFraction	0.176	0.005	0.182
preFilter	0.026	0.004	0.030
removeAnnoationData	0.901	0.030	0.932
subsetSwitchAnalyzeRlist	0.030	0.004	0.035
switchAnalyzeRlist	1.036	0.009	1.051
switchPlot	2.914	0.019	2.945
switchPlotTranscript	0.947	0.009	0.962
testData	0.015	0.005	0.021