Package: IsoformSwitchAnalyzeR

Version: 1.5.6

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_1.5.6.tar.gz

StartedAt: 2019-04-09 01:43:55 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 01:52:17 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 501.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: IsoformSwitchAnalyzeR.Rcheck

Warnings: 2

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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_1.5.6.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/IsoformSwitchAnalyzeR.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.5.6’
* 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-3.9-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 ... 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’
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’
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:
  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 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 ... WARNING
Codoc mismatches from documentation object 'extractConsequenceEnrichment':
extractConsequenceEnrichment
  Code: function(switchAnalyzeRlist, consequencesToAnalyze = "all",
                 alpha = 0.05, dIFcutoff = 0.1,
                 analysisOppositeConsequence = FALSE, plot = TRUE,
                 localTheme = theme_bw(base_size = 12), returnResult =
                 FALSE, returnSummary = TRUE)
  Docs: function(switchAnalyzeRlist, consequencesToAnalyze = "all",
                 alpha = 0.05, dIFcutoff = 0.1, countGenes = TRUE,
                 analysisOppositeConsequence = FALSE, plot = TRUE,
                 localTheme = theme_bw(base_size = 12),
                 minEventsForPlotting = 10, returnResult = TRUE,
                 returnSummary = TRUE)
  Argument names in docs not in code:
    countGenes minEventsForPlotting
  Mismatches in argument names (first 3):
    Position: 5 Code: analysisOppositeConsequence Docs: countGenes
    Position: 6 Code: plot Docs: analysisOppositeConsequence
    Position: 7 Code: localTheme Docs: plot
  Mismatches in argument default values:
    Name: 'returnResult' Code: FALSE Docs: TRUE

Codoc mismatches from documentation object 'extractConsequenceEnrichmentComparison':
extractConsequenceEnrichmentComparison
  Code: function(switchAnalyzeRlist, consequencesToAnalyze = "all",
                 alpha = 0.05, dIFcutoff = 0.1,
                 analysisOppositeConsequence = FALSE, plot = TRUE,
                 localTheme = theme_bw(base_size = 14), returnResult =
                 TRUE)
  Docs: function(switchAnalyzeRlist, consequencesToAnalyze = "all",
                 alpha = 0.05, dIFcutoff = 0.1, countGenes = TRUE,
                 analysisOppositeConsequence = FALSE, plot = TRUE,
                 localTheme = theme_bw(base_size = 14),
                 minEventsForPlotting = 10, returnResult = TRUE)
  Argument names in docs not in code:
    countGenes minEventsForPlotting
  Mismatches in argument names (first 3):
    Position: 5 Code: analysisOppositeConsequence Docs: countGenes
    Position: 6 Code: plot Docs: analysisOppositeConsequence
    Position: 7 Code: localTheme Docs: plot

Codoc mismatches from documentation object 'extractConsequenceSummary':
extractConsequenceSummary
  Code: function(switchAnalyzeRlist, consequencesToAnalyze = "all",
                 includeCombined = FALSE, asFractionTotal = FALSE,
                 alpha = 0.05, dIFcutoff = 0.1, plot = TRUE, plotGenes
                 = FALSE, localTheme = theme_bw(), returnResult =
                 FALSE)
  Docs: function(switchAnalyzeRlist, consequencesToAnalyze = "all",
                 includeCombined = FALSE, asFractionTotal = FALSE,
                 alpha = 0.05, dIFcutoff = 0.1, plot = TRUE, plotGenes
                 = FALSE, simplifyLocation = TRUE, localTheme =
                 theme_bw(), returnResult = FALSE)
  Argument names in docs not in code:
    simplifyLocation
  Mismatches in argument names:
    Position: 9 Code: localTheme Docs: simplifyLocation
    Position: 10 Code: returnResult Docs: localTheme

* 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       33.041  0.431  33.649
importCufflinksGalaxyData     16.605  0.081  16.785
isoformSwitchAnalysisCombined 15.377  0.350  15.838
analyzeAlternativSplicing     11.668  0.048  12.098
IsoformSwitchTestDRIMSeq       9.197  0.051   9.324
analyzeORF                     8.614  0.043   8.711
extractSequence                8.020  0.052   8.086
isoformSwitchAnalysisPart1     7.787  0.038   7.913
isoformSwitchAnalysisPart2     7.053  0.166   7.285
extractTopSwitches             7.166  0.039   7.226
extractSwitchSummary           6.491  0.025   6.541
* 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 WARNINGs, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/IsoformSwitchAnalyzeR.Rcheck/00check.log’
for details.

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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/3.6/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/3.6/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	33.041	0.431	33.649
IsoformSwitchTestDRIMSeq	9.197	0.051	9.324
analyzeAlternativSplicing	11.668	0.048	12.098
analyzeCPAT	0.051	0.007	0.058
analyzeCPC2	0.044	0.005	0.050
analyzeNetSurf2	1.537	0.049	1.613
analyzeORF	8.614	0.043	8.711
analyzePFAM	0.691	0.008	0.704
analyzeSignalP	0.095	0.007	0.103
analyzeSwitchConsequences	1.211	0.016	1.234
expressionAnalysisPlots	1.478	0.009	1.492
extractConsequenceEnrichment	0.685	0.007	0.696
extractConsequenceEnrichmentComparison	1.195	0.010	1.212
extractConsequenceSummary	1.092	0.011	1.114
extractExpressionMatrix	0.291	0.009	0.300
extractGenomeWideAnalysis	4.158	0.100	4.275
extractGenomeWideSplicingAnalysis	3.104	0.092	3.204
extractSequence	8.020	0.052	8.086
extractSplicingEnrichment	1.920	0.025	1.948
extractSplicingEnrichmentComparison	2.311	0.012	2.328
extractSplicingSummary	1.433	0.009	1.445
extractSwitchOverlap	0.467	0.017	0.486
extractSwitchSummary	6.491	0.025	6.541
extractTopSwitches	7.166	0.039	7.226
getCDS	0	0	0
importCufflinksGalaxyData	16.605	0.081	16.785
importGTF	0.411	0.001	0.415
importIsoformExpression	0.039	0.003	0.042
importRdata	1.204	0.012	1.232
isoformSwitchAnalysisCombined	15.377	0.350	15.838
isoformSwitchAnalysisPart1	7.787	0.038	7.913
isoformSwitchAnalysisPart2	7.053	0.166	7.285
isoformToGeneExp	0.211	0.006	0.220
isoformToIsoformFraction	0.215	0.006	0.227
preFilter	0.055	0.007	0.061
subsetSwitchAnalyzeRlist	0.052	0.007	0.059
switchAnalyzeRlist	1.390	0.018	1.423
switchPlot	4.359	0.023	4.434
switchPlotTranscript	2.062	0.011	2.091
testData	0.041	0.007	0.048