Package: CoGAPS

Version: 3.4.1

Command: rm -rf CoGAPS.buildbin-libdir && mkdir CoGAPS.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CoGAPS.buildbin-libdir CoGAPS_3.4.1.tar.gz

StartedAt: 2019-10-16 08:57:12 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 09:02:40 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 328.2 seconds

RetCode: 0

Status:  OK

PackageFile: CoGAPS_3.4.1.zip

PackageFileSize: 20.7 MiB

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###
### Running command:
###
###   rm -rf CoGAPS.buildbin-libdir && mkdir CoGAPS.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CoGAPS.buildbin-libdir CoGAPS_3.4.1.tar.gz
###
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install for i386

* installing *source* package 'CoGAPS' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c Cogaps.cpp -o Cogaps.o
In file included from GapsStatistics.h:5:0,
                 from GapsResult.h:4,
                 from GapsRunner.h:4,
                 from Cogaps.cpp:1:
gibbs_sampler/GibbsSampler.h:178:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
         #pragma omp parallel for num_threads(nThreads)
 ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c GapsParameters.cpp -o GapsParameters.o
GapsParameters.cpp: In member function 'void GapsParameters::print() const':
GapsParameters.cpp:61:76: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type {aka unsigned int}' [-Wformat=]
     gaps_printf("dataIndicesSubset.size(): %lu\n", dataIndicesSubset.size());
                                                                            ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c GapsResult.cpp -o GapsResult.o
In file included from GapsStatistics.h:5:0,
                 from GapsResult.h:4,
                 from GapsResult.cpp:1:
gibbs_sampler/GibbsSampler.h:178:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
         #pragma omp parallel for num_threads(nThreads)
 ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c GapsRunner.cpp -o GapsRunner.o
In file included from GapsStatistics.h:5:0,
                 from GapsResult.h:4,
                 from GapsRunner.h:4,
                 from GapsRunner.cpp:1:
gibbs_sampler/GibbsSampler.h:178:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
         #pragma omp parallel for num_threads(nThreads)
 ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c GapsStatistics.cpp -o GapsStatistics.o
In file included from GapsStatistics.h:5:0,
                 from GapsStatistics.cpp:1:
gibbs_sampler/GibbsSampler.h:178:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
         #pragma omp parallel for num_threads(nThreads)
 ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c test-runner.cpp -o test-runner.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c atomic/AtomicDomain.cpp -o atomic/AtomicDomain.o
atomic/AtomicDomain.cpp:153:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
     #pragma omp critical(AtomicInsertOrErase)
 ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c atomic/ProposalQueue.cpp -o atomic/ProposalQueue.o
atomic/ProposalQueue.cpp:101:0: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
     #pragma omp atomic
 ^
atomic/ProposalQueue.cpp:107:0: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
     #pragma omp atomic
 ^
atomic/ProposalQueue.cpp:113:0: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
     #pragma omp atomic
 ^
atomic/ProposalQueue.cpp:119:0: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
     #pragma omp atomic
 ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c data_structures/HashSets.cpp -o data_structures/HashSets.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c data_structures/HybridMatrix.cpp -o data_structures/HybridMatrix.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c data_structures/HybridVector.cpp -o data_structures/HybridVector.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c data_structures/Matrix.cpp -o data_structures/Matrix.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c data_structures/SparseIterator.cpp -o data_structures/SparseIterator.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c data_structures/SparseMatrix.cpp -o data_structures/SparseMatrix.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c data_structures/SparseVector.cpp -o data_structures/SparseVector.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c data_structures/Vector.cpp -o data_structures/Vector.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c file_parser/CsvParser.cpp -o file_parser/CsvParser.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c file_parser/GctParser.cpp -o file_parser/GctParser.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c file_parser/FileParser.cpp -o file_parser/FileParser.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c file_parser/TsvParser.cpp -o file_parser/TsvParser.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c file_parser/MtxParser.cpp -o file_parser/MtxParser.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c gibbs_sampler/AlphaParameters.cpp -o gibbs_sampler/AlphaParameters.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c gibbs_sampler/DenseStoragePolicy.cpp -o gibbs_sampler/DenseStoragePolicy.o
gibbs_sampler/DenseStoragePolicy.cpp:30:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
     #pragma omp parallel for num_threads(nThreads)
 ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c gibbs_sampler/SparseStoragePolicy.cpp -o gibbs_sampler/SparseStoragePolicy.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c math/Math.cpp -o math/Math.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c math/MatrixMath.cpp -o math/MatrixMath.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c math/Random.cpp -o math/Random.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c math/VectorMath.cpp -o math/VectorMath.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o CoGAPS.dll tmp.def Cogaps.o GapsParameters.o GapsResult.o GapsRunner.o GapsStatistics.o RcppExports.o test-runner.o atomic/AtomicDomain.o atomic/ProposalQueue.o data_structures/HashSets.o data_structures/HybridMatrix.o data_structures/HybridVector.o data_structures/Matrix.o data_structures/SparseIterator.o data_structures/SparseMatrix.o data_structures/SparseVector.o data_structures/Vector.o file_parser/CsvParser.o file_parser/GctParser.o file_parser/FileParser.o file_parser/TsvParser.o file_parser/MtxParser.o gibbs_sampler/AlphaParameters.o gibbs_sampler/DenseStoragePolicy.o gibbs_sampler/SparseStoragePolicy.o math/Math.o math/MatrixMath.o math/Random.o math/VectorMath.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/CoGAPS.buildbin-libdir/00LOCK-CoGAPS/00new/CoGAPS/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CoGAPS'
    finding HTML links ... done
    CoGAPS-package                          html  
    CoGAPS                                  html  
    CogapsParams-class                      html  
    CogapsParams                            html  
    CogapsResult-class                      html  
    GIST.data_frame                         html  
    GIST.matrix                             html  
    GIST.result                             html  
    GIST.uncertainty                        html  
    GWCoGAPS                                html  
    binaryA-methods                         html  
    buildReport                             html  
    calcCoGAPSStat-methods                  html  
    calcGeneGSStat-methods                  html  
    calcZ-methods                           html  
    callInternalCoGAPS                      html  
    checkDataMatrix                         html  
    checkInputs                             html  
    checkpointsEnabled                      html  
    computeGeneGSProb-methods               html  
    convertDataToMatrix                     html  
    corcut                                  html  
    corrToMeanPattern                       html  
    createCogapsResult                      html  
    createSets                              html  
    distributedCogaps                       html  
    findConsensusMatrix                     html  
    gapsCat                                 html  
    getClusteredPatterns-methods            html  
    getCorrelationToMeanPattern-methods     html  
    getDimNames                             html  
    getFeatureLoadings-methods              html  
    getGeneNames                            html  
    getMeanChiSq-methods                    html  
    getOriginalParameters-methods           html  
    getParam-methods                        html  
    getRetinaSubset                         html  
    getSampleFactors-methods                html  
    getSampleNames                          html  
    getSubsets-methods                      html  
    getUnmatchedPatterns-methods            html  
    getValueOrRds                           html  
    getVersion-methods                      html  
    initialize-CogapsParams-method          html  
    initialize-CogapsResult-method          html  
    isRdsFile                               html  
    ncolHelper                              html  
    nrowHelper                              html  
    parseExtraParams                        html  
    patternMarkers-methods                  html  
    patternMatch                            html  
    plotPatternMarkers-methods              html  
    finding level-2 HTML links ... done

    plotResiduals-methods                   html  
    reconstructGene-methods                 html  
    sampleUniformly                         html  
    sampleWithAnnotationWeights             html  
    sampleWithExplictSets                   html  
    scCoGAPS                                html  
    setAnnotationWeights-methods            html  
    setDistributedParams-methods            html  
    setFixedPatterns-methods                html  
    setParam-methods                        html  
    startupMessage                          html  
    stitchTogether                          html  
    supported                               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 'CoGAPS' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c Cogaps.cpp -o Cogaps.o
In file included from GapsStatistics.h:5:0,
                 from GapsResult.h:4,
                 from GapsRunner.h:4,
                 from Cogaps.cpp:1:
gibbs_sampler/GibbsSampler.h:178:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
         #pragma omp parallel for num_threads(nThreads)
 ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c GapsParameters.cpp -o GapsParameters.o
GapsParameters.cpp: In member function 'void GapsParameters::print() const':
GapsParameters.cpp:61:76: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type {aka long long unsigned int}' [-Wformat=]
     gaps_printf("dataIndicesSubset.size(): %lu\n", dataIndicesSubset.size());
                                                                            ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c GapsResult.cpp -o GapsResult.o
In file included from GapsStatistics.h:5:0,
                 from GapsResult.h:4,
                 from GapsResult.cpp:1:
gibbs_sampler/GibbsSampler.h:178:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
         #pragma omp parallel for num_threads(nThreads)
 ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c GapsRunner.cpp -o GapsRunner.o
In file included from GapsStatistics.h:5:0,
                 from GapsResult.h:4,
                 from GapsRunner.h:4,
                 from GapsRunner.cpp:1:
gibbs_sampler/GibbsSampler.h:178:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
         #pragma omp parallel for num_threads(nThreads)
 ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c GapsStatistics.cpp -o GapsStatistics.o
In file included from GapsStatistics.h:5:0,
                 from GapsStatistics.cpp:1:
gibbs_sampler/GibbsSampler.h:178:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
         #pragma omp parallel for num_threads(nThreads)
 ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c test-runner.cpp -o test-runner.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c atomic/AtomicDomain.cpp -o atomic/AtomicDomain.o
atomic/AtomicDomain.cpp:153:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
     #pragma omp critical(AtomicInsertOrErase)
 ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c atomic/ProposalQueue.cpp -o atomic/ProposalQueue.o
atomic/ProposalQueue.cpp:101:0: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
     #pragma omp atomic
 ^
atomic/ProposalQueue.cpp:107:0: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
     #pragma omp atomic
 ^
atomic/ProposalQueue.cpp:113:0: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
     #pragma omp atomic
 ^
atomic/ProposalQueue.cpp:119:0: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
     #pragma omp atomic
 ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c data_structures/HashSets.cpp -o data_structures/HashSets.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c data_structures/HybridMatrix.cpp -o data_structures/HybridMatrix.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c data_structures/HybridVector.cpp -o data_structures/HybridVector.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c data_structures/Matrix.cpp -o data_structures/Matrix.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c data_structures/SparseIterator.cpp -o data_structures/SparseIterator.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c data_structures/SparseMatrix.cpp -o data_structures/SparseMatrix.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c data_structures/SparseVector.cpp -o data_structures/SparseVector.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c data_structures/Vector.cpp -o data_structures/Vector.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c file_parser/CsvParser.cpp -o file_parser/CsvParser.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c file_parser/GctParser.cpp -o file_parser/GctParser.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c file_parser/FileParser.cpp -o file_parser/FileParser.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c file_parser/TsvParser.cpp -o file_parser/TsvParser.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c file_parser/MtxParser.cpp -o file_parser/MtxParser.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c gibbs_sampler/AlphaParameters.cpp -o gibbs_sampler/AlphaParameters.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c gibbs_sampler/DenseStoragePolicy.cpp -o gibbs_sampler/DenseStoragePolicy.o
gibbs_sampler/DenseStoragePolicy.cpp:30:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
     #pragma omp parallel for num_threads(nThreads)
 ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c gibbs_sampler/SparseStoragePolicy.cpp -o gibbs_sampler/SparseStoragePolicy.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c math/Math.cpp -o math/Math.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c math/MatrixMath.cpp -o math/MatrixMath.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c math/Random.cpp -o math/Random.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mtune=generic -c math/VectorMath.cpp -o math/VectorMath.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o CoGAPS.dll tmp.def Cogaps.o GapsParameters.o GapsResult.o GapsRunner.o GapsStatistics.o RcppExports.o test-runner.o atomic/AtomicDomain.o atomic/ProposalQueue.o data_structures/HashSets.o data_structures/HybridMatrix.o data_structures/HybridVector.o data_structures/Matrix.o data_structures/SparseIterator.o data_structures/SparseMatrix.o data_structures/SparseVector.o data_structures/Vector.o file_parser/CsvParser.o file_parser/GctParser.o file_parser/FileParser.o file_parser/TsvParser.o file_parser/MtxParser.o gibbs_sampler/AlphaParameters.o gibbs_sampler/DenseStoragePolicy.o gibbs_sampler/SparseStoragePolicy.o math/Math.o math/MatrixMath.o math/Random.o math/VectorMath.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/CoGAPS.buildbin-libdir/CoGAPS/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CoGAPS' as CoGAPS_3.4.1.zip
* DONE (CoGAPS)