Package: IsoformSwitchAnalyzeR

Version: 1.6.0

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_1.6.0.tar.gz

StartedAt: 2019-10-16 03:57:19 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 04:08:34 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 675.6 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_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/IsoformSwitchAnalyzeR.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.6.0’
* 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
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       42.886  1.095  44.005
importCufflinksGalaxyData     23.059  0.411  23.485
isoformSwitchAnalysisCombined 19.767  0.837  20.611
analyzeAlternativSplicing     14.767  0.047  15.499
IsoformSwitchTestDRIMSeq      12.860  0.128  13.262
extractSequence               11.711  0.180  11.895
analyzeORF                    10.769  0.126  10.899
extractTopSwitches            10.314  0.070  10.386
extractSwitchSummary           9.872  0.069   9.943
isoformSwitchAnalysisPart1     9.364  0.072   9.436
isoformSwitchAnalysisPart2     8.848  0.367   9.218
extractGenomeWideAnalysis      5.142  0.181   5.324
* 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-3.9-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/3.6/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/3.6/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)

name	user	system	elapsed
IsoformSwitchTestDEXSeq	42.886	1.095	44.005
IsoformSwitchTestDRIMSeq	12.860	0.128	13.262
analyzeAlternativSplicing	14.767	0.047	15.499
analyzeCPAT	0.049	0.006	0.057
analyzeCPC2	0.062	0.009	0.070
analyzeNetSurf2	1.633	0.062	1.700
analyzeORF	10.769	0.126	10.899
analyzePFAM	1.191	0.036	1.253
analyzeSignalP	0.127	0.012	0.138
analyzeSwitchConsequences	1.425	0.031	1.455
expressionAnalysisPlots	1.942	0.017	1.988
extractConsequenceEnrichment	0.825	0.019	0.845
extractConsequenceEnrichmentComparison	1.491	0.013	1.505
extractConsequenceSummary	1.303	0.019	1.323
extractExpressionMatrix	0.344	0.019	0.362
extractGenomeWideAnalysis	5.142	0.181	5.324
extractGenomeWideSplicingAnalysis	4.286	0.244	4.532
extractSequence	11.711	0.180	11.895
extractSplicingEnrichment	2.946	0.038	2.984
extractSplicingEnrichmentComparison	3.756	0.045	3.803
extractSplicingSummary	2.197	0.016	2.213
extractSwitchOverlap	0.640	0.025	0.665
extractSwitchSummary	9.872	0.069	9.943
extractTopSwitches	10.314	0.070	10.386
getCDS	0	0	0
importCufflinksGalaxyData	23.059	0.411	23.485
importGTF	0.531	0.013	0.545
importIsoformExpression	0.110	0.014	0.123
importRdata	1.297	0.033	1.331
isoformSwitchAnalysisCombined	19.767	0.837	20.611
isoformSwitchAnalysisPart1	9.364	0.072	9.436
isoformSwitchAnalysisPart2	8.848	0.367	9.218
isoformToGeneExp	0.188	0.008	0.196
isoformToIsoformFraction	0.227	0.013	0.240
preFilter	0.061	0.010	0.071
subsetSwitchAnalyzeRlist	0.058	0.011	0.069
switchAnalyzeRlist	1.359	0.051	1.411
switchPlot	4.740	0.061	4.801
switchPlotTranscript	2.416	0.021	2.438
testData	0.046	0.013	0.060