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 02:57:39 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 03:08:14 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 635.0 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) (2019-03-18 r76245)
* 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           40.482  0.885  41.634
importCufflinksGalaxyData         21.674  0.343  22.031
isoformSwitchAnalysisCombined     17.795  0.687  18.486
analyzeAlternativSplicing         12.880  0.033  12.940
extractSequence                   11.094  0.121  11.216
analyzeORF                        10.701  0.070  10.775
extractTopSwitches                 9.943  0.101  10.045
IsoformSwitchTestDRIMSeq           9.889  0.097  10.375
isoformSwitchAnalysisPart2         9.166  0.315   9.484
extractSwitchSummary               9.243  0.057   9.302
isoformSwitchAnalysisPart1         8.909  0.069   8.979
extractGenomeWideSplicingAnalysis  5.031  0.214   5.246
* 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’ ...
** using staged installation
** 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/00LOCK-IsoformSwitchAnalyzeR/00new/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 from temporary location
Warning: replacing previous import ‘DEXSeq::plotMA’ by ‘limma::plotMA’ when loading ‘IsoformSwitchAnalyzeR’
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘DEXSeq::plotMA’ by ‘limma::plotMA’ when loading ‘IsoformSwitchAnalyzeR’
** testing if installed package keeps a record of temporary installation path
* DONE (IsoformSwitchAnalyzeR)

name	user	system	elapsed
IsoformSwitchTestDEXSeq	40.482	0.885	41.634
IsoformSwitchTestDRIMSeq	9.889	0.097	10.375
analyzeAlternativSplicing	12.880	0.033	12.940
analyzeCPAT	0.058	0.006	0.065
analyzeCPC2	0.058	0.005	0.063
analyzeNetSurf2	1.787	0.064	1.864
analyzeORF	10.701	0.070	10.775
analyzePFAM	0.896	0.008	0.906
analyzeSignalP	0.137	0.012	0.150
analyzeSwitchConsequences	1.402	0.026	1.428
expressionAnalysisPlots	2.239	0.014	2.255
extractConsequenceEnrichment	0.943	0.013	0.956
extractConsequenceEnrichmentComparison	1.303	0.018	1.321
extractConsequenceSummary	1.081	0.010	1.091
extractExpressionMatrix	0.288	0.015	0.303
extractGenomeWideAnalysis	4.541	0.190	4.733
extractGenomeWideSplicingAnalysis	5.031	0.214	5.246
extractSequence	11.094	0.121	11.216
extractSplicingEnrichment	2.939	0.048	2.988
extractSplicingEnrichmentComparison	3.161	0.042	3.205
extractSplicingSummary	2.210	0.025	2.236
extractSwitchOverlap	0.615	0.051	0.673
extractSwitchSummary	9.243	0.057	9.302
extractTopSwitches	9.943	0.101	10.045
getCDS	0.001	0.001	0.001
importCufflinksGalaxyData	21.674	0.343	22.031
importGTF	0.480	0.002	0.483
importIsoformExpression	0.043	0.005	0.048
importRdata	1.294	0.021	1.317
isoformSwitchAnalysisCombined	17.795	0.687	18.486
isoformSwitchAnalysisPart1	8.909	0.069	8.979
isoformSwitchAnalysisPart2	9.166	0.315	9.484
isoformToGeneExp	0.208	0.035	0.243
isoformToIsoformFraction	0.188	0.012	0.200
preFilter	0.043	0.006	0.050
subsetSwitchAnalyzeRlist	0.044	0.010	0.055
switchAnalyzeRlist	1.083	0.025	1.108
switchPlot	4.192	0.062	4.255
switchPlotTranscript	2.309	0.017	2.327
testData	0.031	0.007	0.038