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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/CoGAPS_3.8.0.tar.gz && rm -rf CoGAPS.buildbin-libdir && mkdir CoGAPS.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CoGAPS.buildbin-libdir CoGAPS_3.8.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL CoGAPS_3.8.0.zip && rm CoGAPS_3.8.0.tar.gz CoGAPS_3.8.0.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
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100 24.0M 100 24.0M 0 0 87.1M 0 --:--:-- --:--:-- --:--:-- 89.2M
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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-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
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:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.11-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-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/CoGAPS.buildbin-libdir/CoGAPS/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CoGAPS' as CoGAPS_3.8.0.zip
* DONE (CoGAPS)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'CoGAPS' successfully unpacked and MD5 sums checked
