############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/CoGAPS_3.12.0.tar.gz && rm -rf CoGAPS.buildbin-libdir && mkdir CoGAPS.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CoGAPS.buildbin-libdir CoGAPS_3.12.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL CoGAPS_3.12.0.zip && rm CoGAPS_3.12.0.tar.gz CoGAPS_3.12.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 5 19.6M 5 1132k 0 0 1620k 0 0:00:12 --:--:-- 0:00:12 1619k 19 19.6M 19 3923k 0 0 2326k 0 0:00:08 0:00:01 0:00:07 2326k 35 19.6M 35 7169k 0 0 2674k 0 0:00:07 0:00:02 0:00:05 2674k 56 19.6M 56 11.0M 0 0 3058k 0 0:00:06 0:00:03 0:00:03 3058k 81 19.6M 81 15.9M 0 0 3485k 0 0:00:05 0:00:04 0:00:01 3485k 100 19.6M 100 19.6M 0 0 3804k 0 0:00:05 0:00:05 --:--:-- 4137k 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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"c:/extsoft/include" -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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"c:/extsoft/include" -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::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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"c:/extsoft/include" -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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"c:/extsoft/include" -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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/replace.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/date_time/date_facet.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/date_time/gregorian/gregorian_io.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/date_time/gregorian/gregorian.hpp:31, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/date_time/posix_time/time_formatters.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time.hpp:24, from GapsRunner.cpp:27: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ GapsRunner.cpp: In instantiation of 'GapsResult runCoGAPSAlgorithm(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with Sampler = AsynchronousGibbsSampler; 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; 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; 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; 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; DataType = std::__cxx11::basic_string]': GapsRunner.cpp:70:73: required from 'GapsResult chooseSampler(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataModel = SparseNormalModel; DataType = std::__cxx11::basic_string]' GapsRunner.cpp:85:48: required from 'GapsResult chooseDataModel(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = std::__cxx11::basic_string]' GapsRunner.cpp:104:27: required from 'GapsResult run_helper(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = std::__cxx11::basic_string]' 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; DataType = std::__cxx11::basic_string]': GapsRunner.cpp:74:71: required from 'GapsResult chooseSampler(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataModel = SparseNormalModel; DataType = std::__cxx11::basic_string]' GapsRunner.cpp:85:48: required from 'GapsResult chooseDataModel(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = std::__cxx11::basic_string]' GapsRunner.cpp:104:27: required from 'GapsResult run_helper(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = std::__cxx11::basic_string]' 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; DataType = std::__cxx11::basic_string]': GapsRunner.cpp:70:73: required from 'GapsResult chooseSampler(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataModel = DenseNormalModel; DataType = std::__cxx11::basic_string]' GapsRunner.cpp:88:43: required from 'GapsResult chooseDataModel(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = std::__cxx11::basic_string]' GapsRunner.cpp:104:27: required from 'GapsResult run_helper(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = std::__cxx11::basic_string]' 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; DataType = std::__cxx11::basic_string]': GapsRunner.cpp:74:71: required from 'GapsResult chooseSampler(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataModel = DenseNormalModel; DataType = std::__cxx11::basic_string]' GapsRunner.cpp:88:43: required from 'GapsResult chooseDataModel(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = std::__cxx11::basic_string]' GapsRunner.cpp:104:27: required from 'GapsResult run_helper(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = std::__cxx11::basic_string]' 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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"c:/extsoft/include" -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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"c:/extsoft/include" -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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"c:/extsoft/include" -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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"c:/extsoft/include" -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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"c:/extsoft/include" -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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"c:/extsoft/include" -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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"c:/extsoft/include" -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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"c:/extsoft/include" -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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"c:/extsoft/include" -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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"c:/extsoft/include" -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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"c:/extsoft/include" -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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"c:/extsoft/include" -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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"c:/extsoft/include" -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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"c:/extsoft/include" -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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"c:/extsoft/include" -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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"c:/extsoft/include" -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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"c:/extsoft/include" -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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"c:/extsoft/include" -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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"c:/extsoft/include" -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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"c:/extsoft/include" -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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"c:/extsoft/include" -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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"c:/extsoft/include" -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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"c:/extsoft/include" -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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c math/Math.cpp -o math/Math.o In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/math/constants/constants.hpp:11, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/math/distributions/exponential.hpp:10, from math/Math.cpp:4: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/math/tools/cxx03_warn.hpp:99:88: note: #pragma message: CAUTION: One or more C++11 features were found to be unavailable BOOST_PRAGMA_MESSAGE("CAUTION: One or more C++11 features were found to be unavailable") ^ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/math/constants/constants.hpp:11, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/math/distributions/exponential.hpp:10, from math/Math.cpp:4: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/math/tools/cxx03_warn.hpp:100:139: note: #pragma message: CAUTION: Compiling Boost.Math in pre-C++11 conformance modes is now deprecated and will be removed from March 2021. BOOST_PRAGMA_MESSAGE("CAUTION: Compiling Boost.Math in pre-C++11 conformance modes is now deprecated and will be removed from March 2021.") ^ C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/math/tools/cxx03_warn.hpp:101:106: note: #pragma message: CAUTION: Define BOOST_MATH_DISABLE_DEPRECATED_03_WARNING to suppress this message. BOOST_PRAGMA_MESSAGE("CAUTION: Define BOOST_MATH_DISABLE_DEPRECATED_03_WARNING to suppress this message.") ^ C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/math/tools/cxx03_warn.hpp:102:108: note: #pragma message: CAUTION: This message was generated due to the define: BOOST_NO_CXX11_THREAD_LOCAL BOOST_PRAGMA_MESSAGE("CAUTION: This message was generated due to the define: " BOOST_MATH_CXX03_WARN_REASON) ^ In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/apply.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/iter_apply.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/find_if_pred.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/find_if.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/find.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/contains_impl.hpp:20, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/contains.hpp:20, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/math/policies/policy.hpp:10, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/math/constants/constants.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/math/distributions/exponential.hpp:10, from math/Math.cpp:4: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"c:/extsoft/include" -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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"c:/extsoft/include" -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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"c:/extsoft/include" -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-3~1.13-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"C:/extsoft/include" -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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"C:/extsoft/include" -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::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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"C:/extsoft/include" -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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"C:/extsoft/include" -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 C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/algorithm/string/replace.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/date_time/date_facet.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/date_time/gregorian/gregorian_io.hpp:16, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/date_time/gregorian/gregorian.hpp:31, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/date_time/posix_time/time_formatters.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time.hpp:24, from GapsRunner.cpp:27: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ GapsRunner.cpp: In instantiation of 'GapsResult runCoGAPSAlgorithm(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with Sampler = AsynchronousGibbsSampler; 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; 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; 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; 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; DataType = std::__cxx11::basic_string]': GapsRunner.cpp:70:73: required from 'GapsResult chooseSampler(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataModel = SparseNormalModel; DataType = std::__cxx11::basic_string]' GapsRunner.cpp:85:48: required from 'GapsResult chooseDataModel(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = std::__cxx11::basic_string]' GapsRunner.cpp:104:27: required from 'GapsResult run_helper(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = std::__cxx11::basic_string]' 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; DataType = std::__cxx11::basic_string]': GapsRunner.cpp:74:71: required from 'GapsResult chooseSampler(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataModel = SparseNormalModel; DataType = std::__cxx11::basic_string]' GapsRunner.cpp:85:48: required from 'GapsResult chooseDataModel(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = std::__cxx11::basic_string]' GapsRunner.cpp:104:27: required from 'GapsResult run_helper(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = std::__cxx11::basic_string]' 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; DataType = std::__cxx11::basic_string]': GapsRunner.cpp:70:73: required from 'GapsResult chooseSampler(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataModel = DenseNormalModel; DataType = std::__cxx11::basic_string]' GapsRunner.cpp:88:43: required from 'GapsResult chooseDataModel(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = std::__cxx11::basic_string]' GapsRunner.cpp:104:27: required from 'GapsResult run_helper(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = std::__cxx11::basic_string]' 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; DataType = std::__cxx11::basic_string]': GapsRunner.cpp:74:71: required from 'GapsResult chooseSampler(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataModel = DenseNormalModel; DataType = std::__cxx11::basic_string]' GapsRunner.cpp:88:43: required from 'GapsResult chooseDataModel(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = std::__cxx11::basic_string]' GapsRunner.cpp:104:27: required from 'GapsResult run_helper(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = std::__cxx11::basic_string]' 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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"C:/extsoft/include" -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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"C:/extsoft/include" -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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"C:/extsoft/include" -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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"C:/extsoft/include" -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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"C:/extsoft/include" -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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"C:/extsoft/include" -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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"C:/extsoft/include" -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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"C:/extsoft/include" -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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"C:/extsoft/include" -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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"C:/extsoft/include" -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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"C:/extsoft/include" -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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"C:/extsoft/include" -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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"C:/extsoft/include" -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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"C:/extsoft/include" -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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"C:/extsoft/include" -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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"C:/extsoft/include" -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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"C:/extsoft/include" -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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"C:/extsoft/include" -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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"C:/extsoft/include" -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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"C:/extsoft/include" -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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"C:/extsoft/include" -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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"C:/extsoft/include" -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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"C:/extsoft/include" -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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c math/Math.cpp -o math/Math.o In file included from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/apply.hpp:24, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/iter_apply.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/find_if_pred.hpp:14, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/find_if.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/find.hpp:17, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/aux_/contains_impl.hpp:20, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/contains.hpp:20, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/math/policies/policy.hpp:10, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/math/constants/constants.hpp:12, from C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/math/distributions/exponential.hpp:10, from math/Math.cpp:4: C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses] failed ************ (Pred::************ ^ C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed ************ (boost::mpl::not_::************ ^ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"C:/extsoft/include" -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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"C:/extsoft/include" -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-3~1.13-/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/BH/include' -I"C:/extsoft/include" -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-3~1.13-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/CoGAPS.buildbin-libdir/CoGAPS/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'CoGAPS' as CoGAPS_3.12.0.zip * DONE (CoGAPS) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'CoGAPS' successfully unpacked and MD5 sums checked