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### Running command:
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###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/JunctionSeq_1.20.0.tar.gz && rm -rf JunctionSeq.buildbin-libdir && mkdir JunctionSeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=JunctionSeq.buildbin-libdir JunctionSeq_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL JunctionSeq_1.20.0.zip && rm JunctionSeq_1.20.0.tar.gz JunctionSeq_1.20.0.zip
###
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install for i386

* installing *source* package 'JunctionSeq' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c DESeq2.cpp -o DESeq2.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o JunctionSeq.dll tmp.def DESeq2.o RcppExports.o -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/JunctionSeq.buildbin-libdir/00LOCK-JunctionSeq/00new/JunctionSeq/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'JunctionSeq'
    finding HTML links ... done
    JunctionSeqCountSet-class               html  
    finding level-2 HTML links ... done

    buildAllPlots                           html  
    buildAllPlotsForGene                    html  
    defaultColorList                        html  
    estimateEffectSizes                     html  
    estimateJunctionSeqDispersions          html  
    estimateJunctionSeqSizeFactors          html  
    fitJunctionSeqDispersionFunction        html  
    plotDispEsts                            html  
    plotJunctionSeqResultsForGene           html  
    plotMA                                  html  
    readAnnotationData                      html  
    readJunctionSeqCounts                   html  
    runJunctionSeqAnalyses                  html  
    setJunctionSeqCompiledSourcePackage     html  
    testForDiffUsage                        html  
    writeBedTrack                           html  
    writeCompleteResults                    html  
** building package indices
** installing vignettes
   'JunctionSeq.Rnw' 
** testing if installed package can be loaded from temporary location
Warning: Package 'JunctionSeq' is deprecated and will be removed from
  Bioconductor version 3.13
** testing if installed package can be loaded from final location
Warning: Package 'JunctionSeq' is deprecated and will be removed from
  Bioconductor version 3.13
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'JunctionSeq' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c DESeq2.cpp -o DESeq2.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o JunctionSeq.dll tmp.def DESeq2.o RcppExports.o -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/JunctionSeq.buildbin-libdir/JunctionSeq/libs/x64
** testing if installed package can be loaded
Warning: Package 'JunctionSeq' is deprecated and will be removed from
  Bioconductor version 3.13
* MD5 sums
packaged installation of 'JunctionSeq' as JunctionSeq_1.20.0.zip
* DONE (JunctionSeq)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'JunctionSeq' successfully unpacked and MD5 sums checked