Package: srnadiff

Version: 1.4.0

Command: rm -rf srnadiff.buildbin-libdir && mkdir srnadiff.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=srnadiff.buildbin-libdir srnadiff_1.4.0.tar.gz

StartedAt: 2019-10-16 10:17:38 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 10:19:24 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 106.8 seconds

RetCode: 0

Status:  OK

PackageFile: srnadiff_1.4.0.zip

PackageFileSize: 2.682 MiB

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### Running command:
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###   rm -rf srnadiff.buildbin-libdir && mkdir srnadiff.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=srnadiff.buildbin-libdir srnadiff_1.4.0.tar.gz
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install for i386

* installing *source* package 'srnadiff' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c rcpp_hmm.cpp -o rcpp_hmm.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c rcpp_naive.cpp -o rcpp_naive.o
rcpp_naive.cpp: In function 'Rcpp::DataFrame rcpp_naive(Rcpp::ListOf > >&, Rcpp::ListOf > >&, Rcpp::IntegerVector&, int, int, int)':
rcpp_naive.cpp:80:13: warning: 'start' may be used uninitialized in this function [-Wmaybe-uninitialized]
             if (addElement(start, iterator.getPosition(), chromosome, starts,
             ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c rcpp_slice.cpp -o rcpp_slice.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c rcpp_utils.cpp -o rcpp_utils.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c srnadiff_init.c -o srnadiff_init.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o srnadiff.dll tmp.def RcppExports.o rcpp_hmm.o rcpp_naive.o rcpp_slice.o rcpp_utils.o srnadiff_init.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/srnadiff.buildbin-libdir/00LOCK-srnadiff/00new/srnadiff/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'srnadiff'
    finding HTML links ... done
    buildDataHmm                            html  
    computePvalues                          html  
    plotRegion                              html  
    rcpp_buildHmm                           html  
    rcpp_naive                              html  
    rcpp_normalization                      html  
    rcpp_slice                              html  
    rcpp_viterbi                            html  
    readAnnotation                          html  
    readMiRBaseMatureAnnotation             html  
    readMiRBasePreAnnotation                html  
    readWholeGenomeAnnotation               html  
    regions-method                          html  
    runAll                                  html  
    runAllAnnotation                        html  
    runAllHmm                               html  
    runAllNaive                             html  
    runAllSlice                             html  
    runHmm                                  html  
    runSlice                                html  
    sRNADiff-class                          html  
    sRNADiffExample                         html  
    sRNADiffExp                             html  
    setEmissionProbabilities-method         html  
    setEmissionThreshold-method             html  
    setMergeDistance-method                 html  
    setMinDepth-method                      html  
    setMinDifferences-method                html  
    setMinOverlap-method                    html  
    setNThreads-method                      html  
    setSizes-method                         html  
    setStrategies-method                    html  
    setTransitionProbabilities-method       html  
    show-sRNADiff-method                    html  
    srnadiff                                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 'srnadiff' ...
** libs
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c rcpp_hmm.cpp -o rcpp_hmm.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c rcpp_naive.cpp -o rcpp_naive.o
rcpp_naive.cpp: In function 'Rcpp::DataFrame rcpp_naive(Rcpp::ListOf > >&, Rcpp::ListOf > >&, Rcpp::IntegerVector&, int, int, int)':
rcpp_naive.cpp:80:13: warning: 'start' may be used uninitialized in this function [-Wmaybe-uninitialized]
             if (addElement(start, iterator.getPosition(), chromosome, starts,
             ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c rcpp_slice.cpp -o rcpp_slice.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c rcpp_utils.cpp -o rcpp_utils.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c srnadiff_init.c -o srnadiff_init.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o srnadiff.dll tmp.def RcppExports.o rcpp_hmm.o rcpp_naive.o rcpp_slice.o rcpp_utils.o srnadiff_init.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/srnadiff.buildbin-libdir/srnadiff/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'srnadiff' as srnadiff_1.4.0.zip
* DONE (srnadiff)