Package: IsoformSwitchAnalyzeR

Version: 1.5.6

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:IsoformSwitchAnalyzeR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings IsoformSwitchAnalyzeR_1.5.6.tar.gz

StartedAt: 2019-04-09 01:28:31 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 01:36:03 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 452.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: IsoformSwitchAnalyzeR.Rcheck

Warnings: 2

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:IsoformSwitchAnalyzeR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings IsoformSwitchAnalyzeR_1.5.6.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/IsoformSwitchAnalyzeR.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (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 ‘/home/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       34.210  0.240  34.551
importCufflinksGalaxyData     14.531  0.032  14.616
isoformSwitchAnalysisCombined 12.600  0.088  12.689
analyzeAlternativSplicing      7.887  0.000   7.888
analyzeORF                     7.296  0.012   7.317
extractSequence                6.759  0.016   6.774
extractTopSwitches             6.530  0.012   6.542
extractSwitchSummary           6.155  0.016   6.260
IsoformSwitchTestDRIMSeq       5.651  0.060   5.710
isoformSwitchAnalysisPart2     5.280  0.024   5.305
isoformSwitchAnalysisPart1     5.140  0.012   5.153
* 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/IsoformSwitchAnalyzeR.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL IsoformSwitchAnalyzeR
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘IsoformSwitchAnalyzeR’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c utils.c -o utils.o
gcc -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o IsoformSwitchAnalyzeR.so utils.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/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	34.210	0.240	34.551
IsoformSwitchTestDRIMSeq	5.651	0.060	5.710
analyzeAlternativSplicing	7.887	0.000	7.888
analyzeCPAT	0.060	0.000	0.069
analyzeCPC2	0.048	0.000	0.049
analyzeNetSurf2	1.403	0.029	1.439
analyzeORF	7.296	0.012	7.317
analyzePFAM	0.646	0.007	0.777
analyzeSignalP	0.071	0.000	0.097
analyzeSwitchConsequences	1.093	0.000	1.092
expressionAnalysisPlots	1.136	0.004	1.140
extractConsequenceEnrichment	0.521	0.000	0.522
extractConsequenceEnrichmentComparison	0.892	0.004	0.896
extractConsequenceSummary	1.008	0.000	1.008
extractExpressionMatrix	0.371	0.004	0.375
extractGenomeWideAnalysis	3.527	0.012	3.539
extractGenomeWideSplicingAnalysis	2.731	0.008	2.744
extractSequence	6.759	0.016	6.774
extractSplicingEnrichment	1.354	0.004	1.358
extractSplicingEnrichmentComparison	1.783	0.000	1.802
extractSplicingSummary	1.668	0.000	1.718
extractSwitchOverlap	0.602	0.000	0.659
extractSwitchSummary	6.155	0.016	6.260
extractTopSwitches	6.530	0.012	6.542
getCDS	0	0	0
importCufflinksGalaxyData	14.531	0.032	14.616
importGTF	0.469	0.000	0.470
importIsoformExpression	0.054	0.000	0.054
importRdata	1.155	0.000	1.267
isoformSwitchAnalysisCombined	12.600	0.088	12.689
isoformSwitchAnalysisPart1	5.140	0.012	5.153
isoformSwitchAnalysisPart2	5.280	0.024	5.305
isoformToGeneExp	0.121	0.000	0.121
isoformToIsoformFraction	0.125	0.000	0.125
preFilter	0.029	0.004	0.033
subsetSwitchAnalyzeRlist	0.038	0.000	0.038
switchAnalyzeRlist	0.709	0.000	0.709
switchPlot	3.557	0.000	3.557
switchPlotTranscript	1.623	0.004	1.628
testData	0.044	0.000	0.044