Package: IsoformSwitchAnalyzeR

Version: 1.6.0

Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/IsoformSwitchAnalyzeR_1.6.0.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_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL IsoformSwitchAnalyzeR_1.6.0.zip && rm IsoformSwitchAnalyzeR_1.6.0.tar.gz IsoformSwitchAnalyzeR_1.6.0.zip

StartedAt: 2019-10-15 20:44:45 -0400 (Tue, 15 Oct 2019)

EndedAt: 2019-10-15 20:46:48 -0400 (Tue, 15 Oct 2019)

EllapsedTime: 122.7 seconds

RetCode: 0

Status:  OK

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### Running command:
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###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/IsoformSwitchAnalyzeR_1.6.0.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_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL IsoformSwitchAnalyzeR_1.6.0.zip && rm IsoformSwitchAnalyzeR_1.6.0.tar.gz IsoformSwitchAnalyzeR_1.6.0.zip
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install for i386

* installing *source* package 'IsoformSwitchAnalyzeR' ...
** using staged installation
** 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
** 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
** testing if installed package can be loaded from final location
** 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
* MD5 sums
packaged installation of 'IsoformSwitchAnalyzeR' as IsoformSwitchAnalyzeR_1.6.0.zip
* DONE (IsoformSwitchAnalyzeR)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'IsoformSwitchAnalyzeR' successfully unpacked and MD5 sums checked