############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL CoGAPS ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’ * installing *source* package ‘CoGAPS’ ... ** using staged installation checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ -std=gnu++14 accepts -g... yes checking how to run the C++ preprocessor... g++ -std=gnu++14 -E checking whether we are using the GNU C++ compiler... (cached) yes checking whether g++ -std=gnu++14 accepts -g... (cached) yes ./configure: line 2721: AX_COMPILER_VENDOR: command not found ./configure: line 2722: AX_COMPILER_VERSION: command not found ./configure: line 2733: AX_OPENMP: command not found building on compiler version Using AVX instructions if available configure: creating ./config.status config.status: creating src/Makevars ** libs g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include -march=native -fpic -g -O2 -Wall -c Cogaps.cpp -o Cogaps.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include -march=native -fpic -g -O2 -Wall -c GapsParameters.cpp -o GapsParameters.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include -march=native -fpic -g -O2 -Wall -c GapsResult.cpp -o GapsResult.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include -march=native -fpic -g -O2 -Wall -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] 105 | #pragma omp parallel for num_threads(nThreads) | In file included from /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13, from /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27, from /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string/replace.hpp:16, from /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/date_time/date_facet.hpp:17, from /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/date_time/gregorian/gregorian_io.hpp:16, from /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/date_time/gregorian/gregorian.hpp:31, from /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/date_time/posix_time/time_formatters.hpp:12, from /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time.hpp:24, from GapsRunner.cpp:27: /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | 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] 430 | 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] g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include -march=native -fpic -g -O2 -Wall -c GapsStatistics.cpp -o GapsStatistics.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include -march=native -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include -march=native -fpic -g -O2 -Wall -c test-runner.cpp -o test-runner.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include -march=native -fpic -g -O2 -Wall -c atomic/Atom.cpp -o atomic/Atom.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include -march=native -fpic -g -O2 -Wall -c atomic/ConcurrentAtom.cpp -o atomic/ConcurrentAtom.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include -march=native -fpic -g -O2 -Wall -c atomic/AtomicDomain.cpp -o atomic/AtomicDomain.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include -march=native -fpic -g -O2 -Wall -c atomic/ConcurrentAtomicDomain.cpp -o atomic/ConcurrentAtomicDomain.o atomic/ConcurrentAtomicDomain.cpp:64: warning: ignoring #pragma omp critical [-Wunknown-pragmas] 64 | #pragma omp critical(AtomicInsertOrErase) | g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include -march=native -fpic -g -O2 -Wall -c atomic/ProposalQueue.cpp -o atomic/ProposalQueue.o atomic/ProposalQueue.cpp:101: warning: ignoring #pragma omp atomic [-Wunknown-pragmas] 101 | #pragma omp atomic | atomic/ProposalQueue.cpp:107: warning: ignoring #pragma omp atomic [-Wunknown-pragmas] 107 | #pragma omp atomic | atomic/ProposalQueue.cpp:113: warning: ignoring #pragma omp atomic [-Wunknown-pragmas] 113 | #pragma omp atomic | atomic/ProposalQueue.cpp:119: warning: ignoring #pragma omp atomic [-Wunknown-pragmas] 119 | #pragma omp atomic | g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include -march=native -fpic -g -O2 -Wall -c data_structures/HashSets.cpp -o data_structures/HashSets.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include -march=native -fpic -g -O2 -Wall -c data_structures/HybridMatrix.cpp -o data_structures/HybridMatrix.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include -march=native -fpic -g -O2 -Wall -c data_structures/HybridVector.cpp -o data_structures/HybridVector.o data_structures/HybridVector.cpp:60: warning: ignoring #pragma omp atomic [-Wunknown-pragmas] 60 | #pragma omp atomic | data_structures/HybridVector.cpp:65: warning: ignoring #pragma omp atomic [-Wunknown-pragmas] 65 | #pragma omp atomic | data_structures/HybridVector.cpp:77: warning: ignoring #pragma omp atomic [-Wunknown-pragmas] 77 | #pragma omp atomic | data_structures/HybridVector.cpp:82: warning: ignoring #pragma omp atomic [-Wunknown-pragmas] 82 | #pragma omp atomic | g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include -march=native -fpic -g -O2 -Wall -c data_structures/Matrix.cpp -o data_structures/Matrix.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include -march=native -fpic -g -O2 -Wall -c data_structures/SparseIterator.cpp -o data_structures/SparseIterator.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include -march=native -fpic -g -O2 -Wall -c data_structures/SparseMatrix.cpp -o data_structures/SparseMatrix.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include -march=native -fpic -g -O2 -Wall -c data_structures/SparseVector.cpp -o data_structures/SparseVector.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include -march=native -fpic -g -O2 -Wall -c data_structures/Vector.cpp -o data_structures/Vector.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include -march=native -fpic -g -O2 -Wall -c file_parser/CharacterDelimitedParser.cpp -o file_parser/CharacterDelimitedParser.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include -march=native -fpic -g -O2 -Wall -c file_parser/FileParser.cpp -o file_parser/FileParser.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include -march=native -fpic -g -O2 -Wall -c file_parser/MatrixElement.cpp -o file_parser/MatrixElement.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include -march=native -fpic -g -O2 -Wall -c file_parser/MtxParser.cpp -o file_parser/MtxParser.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include -march=native -fpic -g -O2 -Wall -c gibbs_sampler/AlphaParameters.cpp -o gibbs_sampler/AlphaParameters.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include -march=native -fpic -g -O2 -Wall -c gibbs_sampler/DenseNormalModel.cpp -o gibbs_sampler/DenseNormalModel.o gibbs_sampler/DenseNormalModel.cpp:26: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] 26 | #pragma omp parallel for num_threads(nThreads) | g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include -march=native -fpic -g -O2 -Wall -c gibbs_sampler/SparseNormalModel.cpp -o gibbs_sampler/SparseNormalModel.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include -march=native -fpic -g -O2 -Wall -c math/Math.cpp -o math/Math.o In file included from /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16, from /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13, from /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27, from /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/lexical_cast.hpp:30, from /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/math/tools/lexical_cast.hpp:12, from /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/math/tools/convert_from_string.hpp:14, from /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/math/constants/constants.hpp:14, from /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/math/distributions/exponential.hpp:10, from math/Math.cpp:4: /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_::************ | ^ g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include -march=native -fpic -g -O2 -Wall -c math/MatrixMath.cpp -o math/MatrixMath.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include -march=native -fpic -g -O2 -Wall -c math/Random.cpp -o math/Random.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include -march=native -fpic -g -O2 -Wall -c math/VectorMath.cpp -o math/VectorMath.o g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.15-bioc/R/lib -L/usr/local/lib -o CoGAPS.so 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 -L/home/biocbuild/bbs-3.15-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.15-bioc/R/library/00LOCK-CoGAPS/00new/CoGAPS/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (CoGAPS)