############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL CoGAPS ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-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 the compiler supports GNU C++... yes checking whether g++ -std=gnu++17 accepts -g... yes checking for g++ -std=gnu++17 option to enable C++11 features... none needed checking how to run the C++ preprocessor... g++ -std=gnu++17 -E checking whether the compiler supports GNU C++... (cached) yes checking whether g++ -std=gnu++17 accepts -g... (cached) yes checking for g++ -std=gnu++17 option to enable C++11 features... (cached) none needed ./configure: line 3246: AX_COMPILER_VENDOR: command not found ./configure: line 3247: AX_COMPILER_VERSION: command not found ./configure: line 3259: AX_OPENMP: command not found building on compiler version configure: creating ./config.status config.status: creating src/Makevars ** libs using C++ compiler: ‘g++ (GCC) 10.3.1’ g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c Cogaps.cpp -o Cogaps.o g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c GapsParameters.cpp -o GapsParameters.o g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c GapsResult.cpp -o GapsResult.o g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -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/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/iterator/iterator_categories.hpp:16, from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/iterator/iterator_facade.hpp:13, from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/range/iterator_range_core.hpp:27, from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/algorithm/string/replace.hpp:16, from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/date_time/date_facet.hpp:17, from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/date_time/gregorian/gregorian_io.hpp:16, from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/date_time/gregorian/gregorian.hpp:31, from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/date_time/posix_time/time_formatters.hpp:12, from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/date_time/posix_time/posix_time.hpp:24, from GapsRunner.cpp:28: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-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++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c GapsStatistics.cpp -o GapsStatistics.o g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c test-runner.cpp -o test-runner.o g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c atomic/Atom.cpp -o atomic/Atom.o g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c atomic/ConcurrentAtom.cpp -o atomic/ConcurrentAtom.o g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c atomic/AtomicDomain.cpp -o atomic/AtomicDomain.o g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -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++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -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++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c data_structures/HashSets.cpp -o data_structures/HashSets.o g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c data_structures/HybridMatrix.cpp -o data_structures/HybridMatrix.o g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -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++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c data_structures/Matrix.cpp -o data_structures/Matrix.o g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c data_structures/SparseIterator.cpp -o data_structures/SparseIterator.o g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c data_structures/SparseMatrix.cpp -o data_structures/SparseMatrix.o g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c data_structures/SparseVector.cpp -o data_structures/SparseVector.o g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c data_structures/Vector.cpp -o data_structures/Vector.o g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c file_parser/CharacterDelimitedParser.cpp -o file_parser/CharacterDelimitedParser.o g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c file_parser/FileParser.cpp -o file_parser/FileParser.o g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c file_parser/MatrixElement.cpp -o file_parser/MatrixElement.o g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c file_parser/MtxParser.cpp -o file_parser/MtxParser.o g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c gibbs_sampler/AlphaParameters.cpp -o gibbs_sampler/AlphaParameters.o g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -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++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c gibbs_sampler/SparseNormalModel.cpp -o gibbs_sampler/SparseNormalModel.o g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c math/Math.cpp -o math/Math.o In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/math/distributions/gamma.hpp:14, from math/Math.cpp:5: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/math/special_functions/gamma.hpp: In instantiation of ‘boost::math::detail::upper_incomplete_gamma_fract::result_type boost::math::detail::upper_incomplete_gamma_fract::operator()() [with T = double; boost::math::detail::upper_incomplete_gamma_fract::result_type = std::pair]’: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/math/tools/fraction.hpp:217:20: required from ‘typename boost::math::tools::detail::fraction_traits::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = double; typename boost::math::tools::detail::fraction_traits::result_type = double; uintmax_t = long unsigned int]’ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/math/tools/fraction.hpp:252:31: required from ‘typename boost::math::tools::detail::fraction_traits::result_type boost::math::tools::continued_fraction_a(Gen&, const U&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = double; typename boost::math::tools::detail::fraction_traits::result_type = double]’ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/math/special_functions/gamma.hpp:314:68: required from ‘T boost::math::detail::upper_gamma_fraction(T, T, T) [with T = double]’ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/math/special_functions/gamma.hpp:1176:44: required from ‘T boost::math::detail::gamma_incomplete_imp(T, T, bool, bool, const Policy&, T*) [with T = double; Policy = boost::math::policies::policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/math/special_functions/gamma.hpp:2130:35: required from ‘boost::math::tools::promote_args_t boost::math::gamma_p(RT1, RT2, const Policy&) [with RT1 = double; RT2 = double; Policy = boost::math::policies::policy; boost::math::tools::promote_args_t = double]’ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/math/distributions/gamma.hpp:194:33: required from ‘RealType boost::math::cdf(const boost::math::gamma_distribution&, const RealType&) [with RealType = double; Policy = boost::math::policies::policy]’ /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/math/distributions/detail/derived_accessors.hpp:123:14: required from ‘typename Distribution::value_type boost::math::cdf(const Distribution&, const RealType&) [with Distribution = boost::math::gamma_distribution<>; RealType = float; typename Distribution::value_type = double]’ math/Math.cpp:52:22: required from here /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/math/special_functions/gamma.hpp:299:16: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 299 | result_type operator()() | ^~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c math/MatrixMath.cpp -o math/MatrixMath.o g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c math/Random.cpp -o math/Random.o g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c math/VectorMath.cpp -o math/VectorMath.o g++ -std=gnu++17 -shared -L/home/biocbuild/R/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/R/R/lib -lR installing to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/00LOCK-CoGAPS/00new/CoGAPS/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/dplyr/libs/dplyr.so': /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/dplyr/libs/dplyr.so) Calls: ... namespaceImport -> loadNamespace -> library.dynam -> dyn.load Execution halted ERROR: lazy loading failed for package ‘CoGAPS’ * removing ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/CoGAPS’ * restoring previous ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/CoGAPS’