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INSTALL report for CoGAPS on tokay1

This page was generated on 2021-05-06 12:30:26 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the CoGAPS package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 350/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CoGAPS 3.10.0  (landing page)
Elana J. Fertig
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/CoGAPS
Branch: RELEASE_3_12
Last Commit: 395fcd3
Last Changed Date: 2020-10-27 10:38:41 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: CoGAPS
Version: 3.10.0
Command: C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/CoGAPS_3.10.0.tar.gz && rm -rf CoGAPS.buildbin-libdir && mkdir CoGAPS.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CoGAPS.buildbin-libdir CoGAPS_3.10.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL CoGAPS_3.10.0.zip && rm CoGAPS_3.10.0.tar.gz CoGAPS_3.10.0.zip
StartedAt: 2021-05-05 17:49:29 -0400 (Wed, 05 May 2021)
EndedAt: 2021-05-05 17:58:48 -0400 (Wed, 05 May 2021)
EllapsedTime: 558.2 seconds
RetCode: 0
Status:   OK   

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/CoGAPS_3.10.0.tar.gz && rm -rf CoGAPS.buildbin-libdir && mkdir CoGAPS.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CoGAPS.buildbin-libdir CoGAPS_3.10.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL CoGAPS_3.10.0.zip && rm CoGAPS_3.10.0.tar.gz CoGAPS_3.10.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 24.0M  100 24.0M    0     0  98.7M      0 --:--:-- --:--:-- --:--:-- 99.2M

install for i386

* installing *source* package 'CoGAPS' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c Cogaps.cpp -o Cogaps.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c GapsParameters.cpp -o GapsParameters.o
GapsParameters.cpp: In member function 'void GapsParameters::print() const':
GapsParameters.cpp:41:17: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector<unsigned int>::size_type' {aka 'unsigned int'} [-Wformat=]
     gaps_printf("dataIndicesSubset.size(): %lu\n", dataIndicesSubset.size());
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  ~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c GapsResult.cpp -o GapsResult.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c GapsRunner.cpp -o GapsRunner.o
In file included from GapsRunner.cpp:8:
gibbs_sampler/AsynchronousGibbsSampler.h:105: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
         #pragma omp parallel for num_threads(nThreads)
 
In file included from include/boost/mpl/aux_/na_assert.hpp:23,
                 from include/boost/mpl/arg.hpp:25,
                 from include/boost/mpl/placeholders.hpp:24,
                 from include/boost/iterator/iterator_categories.hpp:16,
                 from include/boost/iterator/iterator_facade.hpp:13,
                 from include/boost/range/iterator_range_core.hpp:27,
                 from include/boost/algorithm/string/replace.hpp:16,
                 from include/boost/date_time/date_facet.hpp:17,
                 from include/boost/date_time/gregorian/gregorian_io.hpp:16,
                 from include/boost/date_time/gregorian/gregorian.hpp:31,
                 from include/boost/date_time/posix_time/time_formatters.hpp:12,
                 from include/boost/date_time/posix_time/posix_time.hpp:24,
                 from GapsRunner.cpp:27:
include/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
include/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
GapsRunner.cpp: In instantiation of 'GapsResult runCoGAPSAlgorithm(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with Sampler = AsynchronousGibbsSampler<SparseNormalModel>; DataType = Matrix]':
GapsRunner.cpp:70:73:   required from 'GapsResult chooseSampler(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataModel = SparseNormalModel; DataType = Matrix]'
GapsRunner.cpp:85:48:   required from 'GapsResult chooseDataModel(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = Matrix]'
GapsRunner.cpp:104:27:   required from 'GapsResult run_helper(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = Matrix]'
GapsRunner.cpp:113:59:   required from here
GapsRunner.cpp:430:5: warning: enumeration value 'GAPS_ALL_PHASES' not handled in switch [-Wswitch]
     switch (phase)
     ^~~~~~
GapsRunner.cpp: In instantiation of 'GapsResult runCoGAPSAlgorithm(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with Sampler = SingleThreadedGibbsSampler<SparseNormalModel>; DataType = Matrix]':
GapsRunner.cpp:74:71:   required from 'GapsResult chooseSampler(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataModel = SparseNormalModel; DataType = Matrix]'
GapsRunner.cpp:85:48:   required from 'GapsResult chooseDataModel(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = Matrix]'
GapsRunner.cpp:104:27:   required from 'GapsResult run_helper(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = Matrix]'
GapsRunner.cpp:113:59:   required from here
GapsRunner.cpp:430:5: warning: enumeration value 'GAPS_ALL_PHASES' not handled in switch [-Wswitch]
GapsRunner.cpp: In instantiation of 'GapsResult runCoGAPSAlgorithm(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with Sampler = AsynchronousGibbsSampler<DenseNormalModel>; DataType = Matrix]':
GapsRunner.cpp:70:73:   required from 'GapsResult chooseSampler(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataModel = DenseNormalModel; DataType = Matrix]'
GapsRunner.cpp:88:43:   required from 'GapsResult chooseDataModel(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = Matrix]'
GapsRunner.cpp:104:27:   required from 'GapsResult run_helper(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = Matrix]'
GapsRunner.cpp:113:59:   required from here
GapsRunner.cpp:430:5: warning: enumeration value 'GAPS_ALL_PHASES' not handled in switch [-Wswitch]
GapsRunner.cpp: In instantiation of 'GapsResult runCoGAPSAlgorithm(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with Sampler = SingleThreadedGibbsSampler<DenseNormalModel>; DataType = Matrix]':
GapsRunner.cpp:74:71:   required from 'GapsResult chooseSampler(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataModel = DenseNormalModel; DataType = Matrix]'
GapsRunner.cpp:88:43:   required from 'GapsResult chooseDataModel(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = Matrix]'
GapsRunner.cpp:104:27:   required from 'GapsResult run_helper(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = Matrix]'
GapsRunner.cpp:113:59:   required from here
GapsRunner.cpp:430:5: warning: enumeration value 'GAPS_ALL_PHASES' not handled in switch [-Wswitch]
GapsRunner.cpp: In instantiation of 'GapsResult runCoGAPSAlgorithm(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with Sampler = AsynchronousGibbsSampler<SparseNormalModel>; DataType = std::__cxx11::basic_string<char>]':
GapsRunner.cpp:70:73:   required from 'GapsResult chooseSampler(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataModel = SparseNormalModel; DataType = std::__cxx11::basic_string<char>]'
GapsRunner.cpp:85:48:   required from 'GapsResult chooseDataModel(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = std::__cxx11::basic_string<char>]'
GapsRunner.cpp:104:27:   required from 'GapsResult run_helper(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = std::__cxx11::basic_string<char>]'
GapsRunner.cpp:119:59:   required from here
GapsRunner.cpp:430:5: warning: enumeration value 'GAPS_ALL_PHASES' not handled in switch [-Wswitch]
GapsRunner.cpp: In instantiation of 'GapsResult runCoGAPSAlgorithm(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with Sampler = SingleThreadedGibbsSampler<SparseNormalModel>; DataType = std::__cxx11::basic_string<char>]':
GapsRunner.cpp:74:71:   required from 'GapsResult chooseSampler(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataModel = SparseNormalModel; DataType = std::__cxx11::basic_string<char>]'
GapsRunner.cpp:85:48:   required from 'GapsResult chooseDataModel(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = std::__cxx11::basic_string<char>]'
GapsRunner.cpp:104:27:   required from 'GapsResult run_helper(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = std::__cxx11::basic_string<char>]'
GapsRunner.cpp:119:59:   required from here
GapsRunner.cpp:430:5: warning: enumeration value 'GAPS_ALL_PHASES' not handled in switch [-Wswitch]
GapsRunner.cpp: In instantiation of 'GapsResult runCoGAPSAlgorithm(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with Sampler = AsynchronousGibbsSampler<DenseNormalModel>; DataType = std::__cxx11::basic_string<char>]':
GapsRunner.cpp:70:73:   required from 'GapsResult chooseSampler(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataModel = DenseNormalModel; DataType = std::__cxx11::basic_string<char>]'
GapsRunner.cpp:88:43:   required from 'GapsResult chooseDataModel(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = std::__cxx11::basic_string<char>]'
GapsRunner.cpp:104:27:   required from 'GapsResult run_helper(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = std::__cxx11::basic_string<char>]'
GapsRunner.cpp:119:59:   required from here
GapsRunner.cpp:430:5: warning: enumeration value 'GAPS_ALL_PHASES' not handled in switch [-Wswitch]
GapsRunner.cpp: In instantiation of 'GapsResult runCoGAPSAlgorithm(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with Sampler = SingleThreadedGibbsSampler<DenseNormalModel>; DataType = std::__cxx11::basic_string<char>]':
GapsRunner.cpp:74:71:   required from 'GapsResult chooseSampler(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataModel = DenseNormalModel; DataType = std::__cxx11::basic_string<char>]'
GapsRunner.cpp:88:43:   required from 'GapsResult chooseDataModel(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = std::__cxx11::basic_string<char>]'
GapsRunner.cpp:104:27:   required from 'GapsResult run_helper(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = std::__cxx11::basic_string<char>]'
GapsRunner.cpp:119:59:   required from here
GapsRunner.cpp:430:5: warning: enumeration value 'GAPS_ALL_PHASES' not handled in switch [-Wswitch]
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c GapsStatistics.cpp -o GapsStatistics.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c test-runner.cpp -o test-runner.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c atomic/Atom.cpp -o atomic/Atom.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c atomic/ConcurrentAtom.cpp -o atomic/ConcurrentAtom.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c atomic/AtomicDomain.cpp -o atomic/AtomicDomain.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c atomic/ConcurrentAtomicDomain.cpp -o atomic/ConcurrentAtomicDomain.o
atomic/ConcurrentAtomicDomain.cpp:64: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
     #pragma omp critical(AtomicInsertOrErase)
 
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c atomic/ProposalQueue.cpp -o atomic/ProposalQueue.o
atomic/ProposalQueue.cpp:101: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
     #pragma omp atomic
 
atomic/ProposalQueue.cpp:107: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
     #pragma omp atomic
 
atomic/ProposalQueue.cpp:113: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
     #pragma omp atomic
 
atomic/ProposalQueue.cpp:119: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
     #pragma omp atomic
 
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c data_structures/HashSets.cpp -o data_structures/HashSets.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c data_structures/HybridMatrix.cpp -o data_structures/HybridMatrix.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c data_structures/HybridVector.cpp -o data_structures/HybridVector.o
data_structures/HybridVector.cpp:60: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
         #pragma omp atomic
 
data_structures/HybridVector.cpp:65: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
     #pragma omp atomic
 
data_structures/HybridVector.cpp:77: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
         #pragma omp atomic
 
data_structures/HybridVector.cpp:82: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
     #pragma omp atomic
 
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c data_structures/Matrix.cpp -o data_structures/Matrix.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c data_structures/SparseIterator.cpp -o data_structures/SparseIterator.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c data_structures/SparseMatrix.cpp -o data_structures/SparseMatrix.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c data_structures/SparseVector.cpp -o data_structures/SparseVector.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c data_structures/Vector.cpp -o data_structures/Vector.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c file_parser/CharacterDelimitedParser.cpp -o file_parser/CharacterDelimitedParser.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c file_parser/FileParser.cpp -o file_parser/FileParser.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c file_parser/MatrixElement.cpp -o file_parser/MatrixElement.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c file_parser/MtxParser.cpp -o file_parser/MtxParser.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c gibbs_sampler/AlphaParameters.cpp -o gibbs_sampler/AlphaParameters.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c gibbs_sampler/DenseNormalModel.cpp -o gibbs_sampler/DenseNormalModel.o
gibbs_sampler/DenseNormalModel.cpp:26: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
     #pragma omp parallel for num_threads(nThreads)
 
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c gibbs_sampler/SparseNormalModel.cpp -o gibbs_sampler/SparseNormalModel.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c math/Math.cpp -o math/Math.o
In file included from include/boost/mpl/aux_/na_assert.hpp:23,
                 from include/boost/mpl/arg.hpp:25,
                 from include/boost/mpl/placeholders.hpp:24,
                 from include/boost/mpl/apply.hpp:24,
                 from include/boost/mpl/aux_/iter_apply.hpp:17,
                 from include/boost/mpl/aux_/find_if_pred.hpp:14,
                 from include/boost/mpl/find_if.hpp:17,
                 from include/boost/mpl/find.hpp:17,
                 from include/boost/mpl/aux_/contains_impl.hpp:20,
                 from include/boost/mpl/contains.hpp:20,
                 from include/boost/math/policies/policy.hpp:10,
                 from include/boost/math/constants/constants.hpp:11,
                 from include/boost/math/distributions/exponential.hpp:10,
                 from math/Math.cpp:4:
include/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
include/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c math/MatrixMath.cpp -o math/MatrixMath.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c math/Random.cpp -o math/Random.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c math/VectorMath.cpp -o math/VectorMath.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -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/Atom.o atomic/ConcurrentAtom.o atomic/AtomicDomain.o atomic/ConcurrentAtomicDomain.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/CharacterDelimitedParser.o file_parser/FileParser.o file_parser/MatrixElement.o file_parser/MtxParser.o gibbs_sampler/AlphaParameters.o gibbs_sampler/DenseNormalModel.o gibbs_sampler/SparseNormalModel.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-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-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  
    compiledWithOpenMPSupport               html  
    computeGeneGSProb-methods               html  
    convertDataToMatrix                     html  
    corcut                                  html  
    corrToMeanPattern                       html  
    createCogapsResult                      html  
    createSets                              html  
    distributedCogaps                       html  
    findConsensusMatrix                     html  
    gapsCat                                 html  
    getAmplitudeMatrix-methods              html  
    getClusteredPatterns-methods            html  
    getCorrelationToMeanPattern-methods     html  
    getDimNames                             html  
    getFeatureLoadings-methods              html  
    getGeneNames                            html  
    getMeanChiSq-methods                    html  
    getOriginalParameters-methods           html  
    getParam-methods                        html  
    getPatternMatrix-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:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c Cogaps.cpp -o Cogaps.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c GapsParameters.cpp -o GapsParameters.o
GapsParameters.cpp: In member function 'void GapsParameters::print() const':
GapsParameters.cpp:41:17: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector<unsigned int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
     gaps_printf("dataIndicesSubset.size(): %lu\n", dataIndicesSubset.size());
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  ~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c GapsResult.cpp -o GapsResult.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c GapsRunner.cpp -o GapsRunner.o
In file included from GapsRunner.cpp:8:
gibbs_sampler/AsynchronousGibbsSampler.h:105: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
         #pragma omp parallel for num_threads(nThreads)
 
In file included from include/boost/mpl/aux_/na_assert.hpp:23,
                 from include/boost/mpl/arg.hpp:25,
                 from include/boost/mpl/placeholders.hpp:24,
                 from include/boost/iterator/iterator_categories.hpp:16,
                 from include/boost/iterator/iterator_facade.hpp:13,
                 from include/boost/range/iterator_range_core.hpp:27,
                 from include/boost/algorithm/string/replace.hpp:16,
                 from include/boost/date_time/date_facet.hpp:17,
                 from include/boost/date_time/gregorian/gregorian_io.hpp:16,
                 from include/boost/date_time/gregorian/gregorian.hpp:31,
                 from include/boost/date_time/posix_time/time_formatters.hpp:12,
                 from include/boost/date_time/posix_time/posix_time.hpp:24,
                 from GapsRunner.cpp:27:
include/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
include/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
GapsRunner.cpp: In instantiation of 'GapsResult runCoGAPSAlgorithm(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with Sampler = AsynchronousGibbsSampler<SparseNormalModel>; DataType = Matrix]':
GapsRunner.cpp:70:73:   required from 'GapsResult chooseSampler(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataModel = SparseNormalModel; DataType = Matrix]'
GapsRunner.cpp:85:48:   required from 'GapsResult chooseDataModel(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = Matrix]'
GapsRunner.cpp:104:27:   required from 'GapsResult run_helper(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = Matrix]'
GapsRunner.cpp:113:59:   required from here
GapsRunner.cpp:430:5: warning: enumeration value 'GAPS_ALL_PHASES' not handled in switch [-Wswitch]
     switch (phase)
     ^~~~~~
GapsRunner.cpp: In instantiation of 'GapsResult runCoGAPSAlgorithm(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with Sampler = SingleThreadedGibbsSampler<SparseNormalModel>; DataType = Matrix]':
GapsRunner.cpp:74:71:   required from 'GapsResult chooseSampler(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataModel = SparseNormalModel; DataType = Matrix]'
GapsRunner.cpp:85:48:   required from 'GapsResult chooseDataModel(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = Matrix]'
GapsRunner.cpp:104:27:   required from 'GapsResult run_helper(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = Matrix]'
GapsRunner.cpp:113:59:   required from here
GapsRunner.cpp:430:5: warning: enumeration value 'GAPS_ALL_PHASES' not handled in switch [-Wswitch]
GapsRunner.cpp: In instantiation of 'GapsResult runCoGAPSAlgorithm(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with Sampler = AsynchronousGibbsSampler<DenseNormalModel>; DataType = Matrix]':
GapsRunner.cpp:70:73:   required from 'GapsResult chooseSampler(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataModel = DenseNormalModel; DataType = Matrix]'
GapsRunner.cpp:88:43:   required from 'GapsResult chooseDataModel(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = Matrix]'
GapsRunner.cpp:104:27:   required from 'GapsResult run_helper(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = Matrix]'
GapsRunner.cpp:113:59:   required from here
GapsRunner.cpp:430:5: warning: enumeration value 'GAPS_ALL_PHASES' not handled in switch [-Wswitch]
GapsRunner.cpp: In instantiation of 'GapsResult runCoGAPSAlgorithm(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with Sampler = SingleThreadedGibbsSampler<DenseNormalModel>; DataType = Matrix]':
GapsRunner.cpp:74:71:   required from 'GapsResult chooseSampler(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataModel = DenseNormalModel; DataType = Matrix]'
GapsRunner.cpp:88:43:   required from 'GapsResult chooseDataModel(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = Matrix]'
GapsRunner.cpp:104:27:   required from 'GapsResult run_helper(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = Matrix]'
GapsRunner.cpp:113:59:   required from here
GapsRunner.cpp:430:5: warning: enumeration value 'GAPS_ALL_PHASES' not handled in switch [-Wswitch]
GapsRunner.cpp: In instantiation of 'GapsResult runCoGAPSAlgorithm(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with Sampler = AsynchronousGibbsSampler<SparseNormalModel>; DataType = std::__cxx11::basic_string<char>]':
GapsRunner.cpp:70:73:   required from 'GapsResult chooseSampler(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataModel = SparseNormalModel; DataType = std::__cxx11::basic_string<char>]'
GapsRunner.cpp:85:48:   required from 'GapsResult chooseDataModel(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = std::__cxx11::basic_string<char>]'
GapsRunner.cpp:104:27:   required from 'GapsResult run_helper(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = std::__cxx11::basic_string<char>]'
GapsRunner.cpp:119:59:   required from here
GapsRunner.cpp:430:5: warning: enumeration value 'GAPS_ALL_PHASES' not handled in switch [-Wswitch]
GapsRunner.cpp: In instantiation of 'GapsResult runCoGAPSAlgorithm(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with Sampler = SingleThreadedGibbsSampler<SparseNormalModel>; DataType = std::__cxx11::basic_string<char>]':
GapsRunner.cpp:74:71:   required from 'GapsResult chooseSampler(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataModel = SparseNormalModel; DataType = std::__cxx11::basic_string<char>]'
GapsRunner.cpp:85:48:   required from 'GapsResult chooseDataModel(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = std::__cxx11::basic_string<char>]'
GapsRunner.cpp:104:27:   required from 'GapsResult run_helper(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = std::__cxx11::basic_string<char>]'
GapsRunner.cpp:119:59:   required from here
GapsRunner.cpp:430:5: warning: enumeration value 'GAPS_ALL_PHASES' not handled in switch [-Wswitch]
GapsRunner.cpp: In instantiation of 'GapsResult runCoGAPSAlgorithm(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with Sampler = AsynchronousGibbsSampler<DenseNormalModel>; DataType = std::__cxx11::basic_string<char>]':
GapsRunner.cpp:70:73:   required from 'GapsResult chooseSampler(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataModel = DenseNormalModel; DataType = std::__cxx11::basic_string<char>]'
GapsRunner.cpp:88:43:   required from 'GapsResult chooseDataModel(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = std::__cxx11::basic_string<char>]'
GapsRunner.cpp:104:27:   required from 'GapsResult run_helper(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = std::__cxx11::basic_string<char>]'
GapsRunner.cpp:119:59:   required from here
GapsRunner.cpp:430:5: warning: enumeration value 'GAPS_ALL_PHASES' not handled in switch [-Wswitch]
GapsRunner.cpp: In instantiation of 'GapsResult runCoGAPSAlgorithm(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with Sampler = SingleThreadedGibbsSampler<DenseNormalModel>; DataType = std::__cxx11::basic_string<char>]':
GapsRunner.cpp:74:71:   required from 'GapsResult chooseSampler(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataModel = DenseNormalModel; DataType = std::__cxx11::basic_string<char>]'
GapsRunner.cpp:88:43:   required from 'GapsResult chooseDataModel(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = std::__cxx11::basic_string<char>]'
GapsRunner.cpp:104:27:   required from 'GapsResult run_helper(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = std::__cxx11::basic_string<char>]'
GapsRunner.cpp:119:59:   required from here
GapsRunner.cpp:430:5: warning: enumeration value 'GAPS_ALL_PHASES' not handled in switch [-Wswitch]
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c GapsStatistics.cpp -o GapsStatistics.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c test-runner.cpp -o test-runner.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c atomic/Atom.cpp -o atomic/Atom.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c atomic/ConcurrentAtom.cpp -o atomic/ConcurrentAtom.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c atomic/AtomicDomain.cpp -o atomic/AtomicDomain.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c atomic/ConcurrentAtomicDomain.cpp -o atomic/ConcurrentAtomicDomain.o
atomic/ConcurrentAtomicDomain.cpp:64: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
     #pragma omp critical(AtomicInsertOrErase)
 
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c atomic/ProposalQueue.cpp -o atomic/ProposalQueue.o
atomic/ProposalQueue.cpp:101: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
     #pragma omp atomic
 
atomic/ProposalQueue.cpp:107: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
     #pragma omp atomic
 
atomic/ProposalQueue.cpp:113: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
     #pragma omp atomic
 
atomic/ProposalQueue.cpp:119: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
     #pragma omp atomic
 
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c data_structures/HashSets.cpp -o data_structures/HashSets.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c data_structures/HybridMatrix.cpp -o data_structures/HybridMatrix.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c data_structures/HybridVector.cpp -o data_structures/HybridVector.o
data_structures/HybridVector.cpp:60: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
         #pragma omp atomic
 
data_structures/HybridVector.cpp:65: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
     #pragma omp atomic
 
data_structures/HybridVector.cpp:77: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
         #pragma omp atomic
 
data_structures/HybridVector.cpp:82: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
     #pragma omp atomic
 
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c data_structures/Matrix.cpp -o data_structures/Matrix.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c data_structures/SparseIterator.cpp -o data_structures/SparseIterator.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c data_structures/SparseMatrix.cpp -o data_structures/SparseMatrix.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c data_structures/SparseVector.cpp -o data_structures/SparseVector.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c data_structures/Vector.cpp -o data_structures/Vector.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c file_parser/CharacterDelimitedParser.cpp -o file_parser/CharacterDelimitedParser.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c file_parser/FileParser.cpp -o file_parser/FileParser.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c file_parser/MatrixElement.cpp -o file_parser/MatrixElement.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c file_parser/MtxParser.cpp -o file_parser/MtxParser.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c gibbs_sampler/AlphaParameters.cpp -o gibbs_sampler/AlphaParameters.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c gibbs_sampler/DenseNormalModel.cpp -o gibbs_sampler/DenseNormalModel.o
gibbs_sampler/DenseNormalModel.cpp:26: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
     #pragma omp parallel for num_threads(nThreads)
 
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c gibbs_sampler/SparseNormalModel.cpp -o gibbs_sampler/SparseNormalModel.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c math/Math.cpp -o math/Math.o
In file included from include/boost/mpl/aux_/na_assert.hpp:23,
                 from include/boost/mpl/arg.hpp:25,
                 from include/boost/mpl/placeholders.hpp:24,
                 from include/boost/mpl/apply.hpp:24,
                 from include/boost/mpl/aux_/iter_apply.hpp:17,
                 from include/boost/mpl/aux_/find_if_pred.hpp:14,
                 from include/boost/mpl/find_if.hpp:17,
                 from include/boost/mpl/find.hpp:17,
                 from include/boost/mpl/aux_/contains_impl.hpp:20,
                 from include/boost/mpl/contains.hpp:20,
                 from include/boost/math/policies/policy.hpp:10,
                 from include/boost/math/constants/constants.hpp:11,
                 from include/boost/math/distributions/exponential.hpp:10,
                 from math/Math.cpp:4:
include/boost/mpl/assert.hpp:188:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
include/boost/mpl/assert.hpp:193:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c math/MatrixMath.cpp -o math/MatrixMath.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c math/Random.cpp -o math/Random.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"  -march=native   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c math/VectorMath.cpp -o math/VectorMath.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -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/Atom.o atomic/ConcurrentAtom.o atomic/AtomicDomain.o atomic/ConcurrentAtomicDomain.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/CharacterDelimitedParser.o file_parser/FileParser.o file_parser/MatrixElement.o file_parser/MtxParser.o gibbs_sampler/AlphaParameters.o gibbs_sampler/DenseNormalModel.o gibbs_sampler/SparseNormalModel.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-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/CoGAPS.buildbin-libdir/CoGAPS/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CoGAPS' as CoGAPS_3.10.0.zip
* DONE (CoGAPS)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'CoGAPS' successfully unpacked and MD5 sums checked