Package: IsoformSwitchAnalyzeR

Version: 1.5.6

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:IsoformSwitchAnalyzeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings IsoformSwitchAnalyzeR_1.5.6.tar.gz

StartedAt: 2019-04-09 03:45:12 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 03:56:58 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 706.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: IsoformSwitchAnalyzeR.Rcheck

Warnings: 2

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:IsoformSwitchAnalyzeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings IsoformSwitchAnalyzeR_1.5.6.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/IsoformSwitchAnalyzeR.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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 'C:/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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/IsoformSwitchAnalyzeR/libs/i386/IsoformSwitchAnalyzeR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/IsoformSwitchAnalyzeR/libs/x64/IsoformSwitchAnalyzeR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
IsoformSwitchTestDEXSeq       32.99   1.48   34.61
importCufflinksGalaxyData     14.10   0.13   14.64
isoformSwitchAnalysisCombined 11.84   0.13   11.99
analyzeAlternativSplicing      9.41   0.03    9.44
extractSequence                8.46   0.03    8.49
analyzeORF                     7.75   0.19    7.95
extractTopSwitches             6.73   0.05    6.78
IsoformSwitchTestDRIMSeq       6.06   0.02    6.07
isoformSwitchAnalysisPart2     5.41   0.12    5.54
isoformSwitchAnalysisPart1     5.20   0.00    5.20
extractSwitchSummary           5.06   0.02    5.08
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
IsoformSwitchTestDEXSeq       30.78   0.18   31.03
importCufflinksGalaxyData     14.11   0.03   14.14
isoformSwitchAnalysisCombined 12.47   0.14   12.61
analyzeAlternativSplicing      9.53   0.01    9.55
extractSequence                9.11   0.00    9.11
analyzeORF                     8.54   0.01    8.58
isoformSwitchAnalysisPart1     7.88   0.09    7.97
extractTopSwitches             6.91   0.01    6.92
isoformSwitchAnalysisPart2     5.84   0.12    5.98
IsoformSwitchTestDRIMSeq       5.90   0.03    5.92
extractSwitchSummary           5.41   0.02    5.42
* 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
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/IsoformSwitchAnalyzeR.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/IsoformSwitchAnalyzeR_1.5.6.tar.gz && rm -rf IsoformSwitchAnalyzeR.buildbin-libdir && mkdir IsoformSwitchAnalyzeR.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=IsoformSwitchAnalyzeR.buildbin-libdir IsoformSwitchAnalyzeR_1.5.6.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL IsoformSwitchAnalyzeR_1.5.6.zip && rm IsoformSwitchAnalyzeR_1.5.6.tar.gz IsoformSwitchAnalyzeR_1.5.6.zip
###
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100 2805k  100 2805k    0     0  34.5M      0 --:--:-- --:--:-- --:--:-- 38.0M

install for i386

* installing *source* package 'IsoformSwitchAnalyzeR' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c utils.c -o utils.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o IsoformSwitchAnalyzeR.dll tmp.def utils.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/IsoformSwitchAnalyzeR.buildbin-libdir/00LOCK-IsoformSwitchAnalyzeR/00new/IsoformSwitchAnalyzeR/libs/i386
** 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
  converting help for package 'IsoformSwitchAnalyzeR'
    finding HTML links ... done
    CDSSet                                  html  
    IsoformSwitchTestDEXSeq                 html  
    IsoformSwitchTestDRIMSeq                html  
    finding level-2 HTML links ... done

    analyzeAlternativSplicing               html  
    analyzeCPAT                             html  
    analyzeCPC2                             html  
    analyzeNetSurf2                         html  
    analyzeORF                              html  
    analyzePFAM                             html  
    analyzeSignalP                          html  
    analyzeSwitchConsequences               html  
    expressionAnalysisPlots                 html  
    extractConsequenceEnrichment            html  
    extractConsequenceEnrichmentComparison
                                            html  
    extractConsequenceSummary               html  
    extractExpressionMatrix                 html  
    extractGenomeWideAnalysis               html  
    extractGenomeWideSplicingAnalysis       html  
    extractSequence                         html  
    extractSplicingEnrichment               html  
    extractSplicingEnrichmentComparison     html  
    extractSplicingSummary                  html  
    extractSwitchOverlap                    html  
    extractSwitchSummary                    html  
    extractTopSwitches                      html  
    getCDS                                  html  
    importCufflinksGalaxyData               html  
    importGTF                               html  
    importIsoformExpression                 html  
    importRdata                             html  
    isoformSwitchAnalysisCombined           html  
    isoformSwitchAnalysisPart1              html  
    isoformSwitchAnalysisPart2              html  
    isoformToGeneExp                        html  
    isoformToIsoformFraction                html  
    preFilter                               html  
    subsetSwitchAnalyzeRlist                html  
    switchAnalyzeRlist                      html  
    switchPlot                              html  
    switchPlotTopSwitches                   html  
    switchPlotTranscript                    html  
    testData                                html  
** 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'
** 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

install for x64

* installing *source* package 'IsoformSwitchAnalyzeR' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c utils.c -o utils.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o IsoformSwitchAnalyzeR.dll tmp.def utils.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/IsoformSwitchAnalyzeR.buildbin-libdir/IsoformSwitchAnalyzeR/libs/x64
** testing if installed package can be loaded
Warning: replacing previous import 'DEXSeq::plotMA' by 'limma::plotMA' when loading 'IsoformSwitchAnalyzeR'
* MD5 sums
packaged installation of 'IsoformSwitchAnalyzeR' as IsoformSwitchAnalyzeR_1.5.6.zip
* DONE (IsoformSwitchAnalyzeR)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'IsoformSwitchAnalyzeR' successfully unpacked and MD5 sums checked