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BUILD BIN report for BitSeq on tokay2

This page was generated on 2019-10-16 12:26:24 -0400 (Wed, 16 Oct 2019).

Package 177/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BitSeq 1.28.0
Antti Honkela , Panagiotis Papastamoulis
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/BitSeq
Branch: RELEASE_3_9
Last Commit: 63856e9
Last Changed Date: 2019-05-02 11:53:35 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS [ OK ]UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: BitSeq
Version: 1.28.0
Command: rm -rf BitSeq.buildbin-libdir && mkdir BitSeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BitSeq.buildbin-libdir BitSeq_1.28.0.tar.gz
StartedAt: 2019-10-16 08:48:16 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 08:50:37 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 140.7 seconds
RetCode: 0
Status:  OK  
PackageFile: BitSeq_1.28.0.zip
PackageFileSize: 2.233 MiB

Command output

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###
### Running command:
###
###   rm -rf BitSeq.buildbin-libdir && mkdir BitSeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BitSeq.buildbin-libdir BitSeq_1.28.0.tar.gz
###
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##############################################################################



install for i386

* installing *source* package 'BitSeq' ...
** using staged installation

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c ArgumentParser.cpp -o ArgumentParser.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c CollapsedSampler.cpp -o CollapsedSampler.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c FileHeader.cpp -o FileHeader.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c GibbsParameters.cpp -o GibbsParameters.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c GibbsSampler.cpp -o GibbsSampler.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c MyTimer.cpp -o MyTimer.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c PosteriorSamples.cpp -o PosteriorSamples.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c R_init_BitSeq.cpp -o R_init_BitSeq.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c ReadDistribution.cpp -o ReadDistribution.o
ReadDistribution.cpp:838:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
       #pragma omp parallel for \
 ^
ReadDistribution.cpp:923:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
    #pragma omp parallel for \
 ^
ReadDistribution.cpp:928:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
          #pragma omp critical
 ^
ReadDistribution.cpp: In function 'long int ns_rD::countDeletions(const bam1_t*)':
ReadDistribution.cpp:66:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for(long i=0;icore.n_cigar;i++){
                  ^
ReadDistribution.cpp: In function 'bool ns_rD::getCigarOp(const bam1_t*, long int, long int*, long int*)':
ReadDistribution.cpp:79:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if((cigarI<0) || (cigarI >= samA->core.n_cigar)) return false;
                             ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c Sampler.cpp -o Sampler.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c SimpleSparse.cpp -o SimpleSparse.o
SimpleSparse.cpp:35:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
    #pragma omp parallel for reduction(+:count)
 ^
SimpleSparse.cpp:45:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
    #pragma omp parallel for private(i,logRowSum)
 ^
SimpleSparse.cpp:57:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
    #pragma omp parallel for private(i,logRowSum)
 ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c TagAlignments.cpp -o TagAlignments.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c TranscriptExpression.cpp -o TranscriptExpression.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c TranscriptInfo.cpp -o TranscriptInfo.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c TranscriptSequence.cpp -o TranscriptSequence.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c VariationalBayes.cpp -o VariationalBayes.o
VariationalBayes.cpp:86:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
       #pragma omp parallel for
 ^
VariationalBayes.cpp:96:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
    #pragma omp parallel for private(err) reduction(+:totalError)
 ^
VariationalBayes.cpp:103:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
    #pragma omp parallel for
 ^
VariationalBayes.cpp:110:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
    #pragma omp parallel for reduction(+:A,B)
 ^
VariationalBayes.cpp:119:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
    #pragma omp parallel for reduction(+:C)
 ^
VariationalBayes.cpp:172:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
       #pragma omp parallel for private(i,phiGradPhiSum_r,natGrad_i,gradGamma_i) reduction(+:squareNorm,valBeta,valBetaDiv)
 ^
VariationalBayes.cpp:219:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
          #pragma omp parallel for
 ^
VariationalBayes.cpp:224:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
          #pragma omp parallel for
 ^
VariationalBayes.cpp:238:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
          #pragma omp parallel for
 ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c bam_plbuf.c -o bam_plbuf.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c common.cpp -o common.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c estimateDE.cpp -o estimateDE.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c estimateExpression.cpp -o estimateExpression.o
estimateExpression.cpp:208:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
       #pragma omp parallel for private(subCounter)
 ^
estimateExpression.cpp:244:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
          #pragma omp parallel for private(subCounter)
 ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c estimateHyperPar.cpp -o estimateHyperPar.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c estimateVBExpression.cpp -o estimateVBExpression.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c getGeneExpression.cpp -o getGeneExpression.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c getVariance.cpp -o getVariance.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c getWithinGeneExpression.cpp -o getWithinGeneExpression.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c lowess.cpp -o lowess.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c misc.cpp -o misc.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c parseAlignment.cpp -o parseAlignment.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c sam.c -o sam.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c transposeFiles.cpp -o transposeFiles.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o BitSeq.dll tmp.def ArgumentParser.o CollapsedSampler.o FileHeader.o GibbsParameters.o GibbsSampler.o MyTimer.o PosteriorSamples.o R_init_BitSeq.o ReadDistribution.o Sampler.o SimpleSparse.o TagAlignments.o TranscriptExpression.o TranscriptInfo.o TranscriptSequence.o VariationalBayes.o bam_plbuf.o common.o estimateDE.o estimateExpression.o estimateHyperPar.o estimateVBExpression.o getGeneExpression.o getVariance.o getWithinGeneExpression.o lowess.o misc.o parseAlignment.o sam.o transposeFiles.o -LC:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/usrlib/i386 -lhts -lz -lm -lws2_32 -lpthread -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/BitSeq.buildbin-libdir/00LOCK-BitSeq/00new/BitSeq/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BitSeq'
    finding HTML links ... done
    BitSeq-package                          html  
    estimateDE                              html  
    estimateExpression                      html  
    estimateHyperPar                        html  
    estimateVBExpression                    html  
    getDE                                   html  
    getExpression                           html  
    getGeneExpression                       html  
    getMeanVariance                         html  
    loadSamples                             html  
    parseAlignment                          html  
    transcriptInfo                          html  
    transcriptInfoFile                      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 'BitSeq' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c ArgumentParser.cpp -o ArgumentParser.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c CollapsedSampler.cpp -o CollapsedSampler.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c FileHeader.cpp -o FileHeader.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c GibbsParameters.cpp -o GibbsParameters.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c GibbsSampler.cpp -o GibbsSampler.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c MyTimer.cpp -o MyTimer.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c PosteriorSamples.cpp -o PosteriorSamples.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c R_init_BitSeq.cpp -o R_init_BitSeq.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c ReadDistribution.cpp -o ReadDistribution.o
ReadDistribution.cpp:838:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
       #pragma omp parallel for \
 ^
ReadDistribution.cpp:923:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
    #pragma omp parallel for \
 ^
ReadDistribution.cpp:928:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
          #pragma omp critical
 ^
ReadDistribution.cpp: In function 'long int ns_rD::countDeletions(const bam1_t*)':
ReadDistribution.cpp:66:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for(long i=0;icore.n_cigar;i++){
                  ^
ReadDistribution.cpp: In function 'bool ns_rD::getCigarOp(const bam1_t*, long int, long int*, long int*)':
ReadDistribution.cpp:79:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if((cigarI<0) || (cigarI >= samA->core.n_cigar)) return false;
                             ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c Sampler.cpp -o Sampler.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c SimpleSparse.cpp -o SimpleSparse.o
SimpleSparse.cpp:35:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
    #pragma omp parallel for reduction(+:count)
 ^
SimpleSparse.cpp:45:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
    #pragma omp parallel for private(i,logRowSum)
 ^
SimpleSparse.cpp:57:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
    #pragma omp parallel for private(i,logRowSum)
 ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c TagAlignments.cpp -o TagAlignments.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c TranscriptExpression.cpp -o TranscriptExpression.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c TranscriptInfo.cpp -o TranscriptInfo.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c TranscriptSequence.cpp -o TranscriptSequence.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c VariationalBayes.cpp -o VariationalBayes.o
VariationalBayes.cpp:86:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
       #pragma omp parallel for
 ^
VariationalBayes.cpp:96:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
    #pragma omp parallel for private(err) reduction(+:totalError)
 ^
VariationalBayes.cpp:103:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
    #pragma omp parallel for
 ^
VariationalBayes.cpp:110:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
    #pragma omp parallel for reduction(+:A,B)
 ^
VariationalBayes.cpp:119:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
    #pragma omp parallel for reduction(+:C)
 ^
VariationalBayes.cpp:172:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
       #pragma omp parallel for private(i,phiGradPhiSum_r,natGrad_i,gradGamma_i) reduction(+:squareNorm,valBeta,valBetaDiv)
 ^
VariationalBayes.cpp:219:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
          #pragma omp parallel for
 ^
VariationalBayes.cpp:224:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
          #pragma omp parallel for
 ^
VariationalBayes.cpp:238:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
          #pragma omp parallel for
 ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c bam_plbuf.c -o bam_plbuf.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c common.cpp -o common.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c estimateDE.cpp -o estimateDE.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c estimateExpression.cpp -o estimateExpression.o
estimateExpression.cpp:208:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
       #pragma omp parallel for private(subCounter)
 ^
estimateExpression.cpp:244:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
          #pragma omp parallel for private(subCounter)
 ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c estimateHyperPar.cpp -o estimateHyperPar.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c estimateVBExpression.cpp -o estimateVBExpression.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c getGeneExpression.cpp -o getGeneExpression.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c getVariance.cpp -o getVariance.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c getWithinGeneExpression.cpp -o getWithinGeneExpression.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c lowess.cpp -o lowess.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c misc.cpp -o misc.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c parseAlignment.cpp -o parseAlignment.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c sam.c -o sam.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c transposeFiles.cpp -o transposeFiles.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o BitSeq.dll tmp.def ArgumentParser.o CollapsedSampler.o FileHeader.o GibbsParameters.o GibbsSampler.o MyTimer.o PosteriorSamples.o R_init_BitSeq.o ReadDistribution.o Sampler.o SimpleSparse.o TagAlignments.o TranscriptExpression.o TranscriptInfo.o TranscriptSequence.o VariationalBayes.o bam_plbuf.o common.o estimateDE.o estimateExpression.o estimateHyperPar.o estimateVBExpression.o getGeneExpression.o getVariance.o getWithinGeneExpression.o lowess.o misc.o parseAlignment.o sam.o transposeFiles.o -LC:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/usrlib/x64 -lhts -lz -lm -lws2_32 -lpthread -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/BitSeq.buildbin-libdir/BitSeq/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BitSeq' as BitSeq_1.28.0.zip
* DONE (BitSeq)