############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf ppcseq.buildbin-libdir && mkdir ppcseq.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ppcseq_1.14.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R ppcseq.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=ppcseq.buildbin-libdir ppcseq_1.14.0.tar.gz' >>>>>>> * installing *source* package ‘ppcseq’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using C++17 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include' -I/opt/R/arm64/include -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable] Index count = 0; ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable] Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable] Index nsuper_et = 0; // Number of relaxed snodes in the original etree ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable] Index replacements = 0; ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:37: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable] int count = 0; ^ 5 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include' -I/opt/R/arm64/include -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -falign-functions=64 -Wall -g -O2 -c stanExports_negBinomial_MPI.cc -o stanExports_negBinomial_MPI.o In file included from stanExports_negBinomial_MPI.cc:5: In file included from ./stanExports_negBinomial_MPI.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable] Index count = 0; ^ In file included from stanExports_negBinomial_MPI.cc:5: In file included from ./stanExports_negBinomial_MPI.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable] Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable] Index nsuper_et = 0; // Number of relaxed snodes in the original etree ^ In file included from stanExports_negBinomial_MPI.cc:5: In file included from ./stanExports_negBinomial_MPI.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:21: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/io/r_ostream.hpp:47:31: warning: 'rstan::io::r_cout_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] virtual std::streamsize xsputn(const char_type* s, int n) { ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/streambuf:291:24: note: hidden overloaded virtual function 'std::basic_streambuf::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int') virtual streamsize xsputn(const char_type* __s, streamsize __n); ^ In file included from stanExports_negBinomial_MPI.cc:5: In file included from ./stanExports_negBinomial_MPI.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:21: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/io/r_ostream.hpp:70:31: warning: 'rstan::io::r_cerr_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] virtual std::streamsize xsputn(const char_type* s, int n) { ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/streambuf:291:24: note: hidden overloaded virtual function 'std::basic_streambuf::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int') virtual streamsize xsputn(const char_type* __s, streamsize __n); ^ In file included from stanExports_negBinomial_MPI.cc:5: In file included from ./stanExports_negBinomial_MPI.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:31: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable] Index replacements = 0; ^ In file included from stanExports_negBinomial_MPI.cc:5: In file included from ./stanExports_negBinomial_MPI.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:31: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:37: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable] int count = 0; ^ In file included from stanExports_negBinomial_MPI.cc:5: In file included from ./stanExports_negBinomial_MPI.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:43: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:35: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:57:1: warning: 'ops_partials_edge' defined as a struct template here but previously declared as a class template; this is valid, but may result in linker errors under the Microsoft C++ ABI [-Wmismatched-tags] struct ops_partials_edge> { ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:45:1: note: did you mean struct here? class ops_partials_edge; ^~~~~ struct In file included from stanExports_negBinomial_MPI.cc:5: In file included from ./stanExports_negBinomial_MPI.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:1252:9: warning: variable 'ret' set but not used [-Wunused-but-set-variable] int ret = stan::services::error_codes::CONFIG; ^ In file included from stanExports_negBinomial_MPI.cc:5: ./stanExports_negBinomial_MPI.h:1422:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable] int pos__ = std::numeric_limits::min(); ^ In file included from stanExports_negBinomial_MPI.cc:5: In file included from ./stanExports_negBinomial_MPI.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:43: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:46: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/choose.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/special_functions/binomial.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/special_functions/beta.hpp:1721: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:29:15: warning: unused variable 'x_extrema' [-Wunused-variable] const T x_extrema = 1 / (1 + a); ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:304:7: note: in instantiation of member function 'boost::math::detail::temme_root_finder::temme_root_finder' requested here temme_root_finder(-lu, alpha), x, lower, upper, policies::digits() / 2); ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:615:20: note: in instantiation of function template specialization 'boost::math::detail::temme_method_2_ibeta_inverse, boost::math::policies::promote_float, boost::math::policies::promote_double>>' requested here x = temme_method_2_ibeta_inverse(a, b, p, r, theta, pol); ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:992:17: note: in instantiation of function template specialization 'boost::math::detail::ibeta_inv_imp, boost::math::policies::promote_float, boost::math::policies::promote_double>>' requested here rx = detail::ibeta_inv_imp( ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:1023:11: note: in instantiation of function template specialization 'boost::math::ibeta_inv, boost::math::policies::pole_error, boost::math::policies::promote_double, boost::math::policies::digits2<>>>' requested here return ibeta_inv(a, b, p, static_cast(nullptr), pol); ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/inv_inc_beta.hpp:32:23: note: in instantiation of function template specialization 'boost::math::ibeta_inv, boost::math::policies::pole_error, boost::math::policies::promote_double, boost::math::policies::digits2<>>>' requested here return boost::math::ibeta_inv(a, b, p, boost_policy_t<>()); ^ In file included from stanExports_negBinomial_MPI.cc:5: ./stanExports_negBinomial_MPI.h:438:15: warning: unused variable 'global_parameters' [-Wunused-variable] const auto& global_parameters = stan::math::to_ref(global_parameters_arg__); ^ ./stanExports_negBinomial_MPI.h:242:12: note: in instantiation of function template specialization 'model_negBinomial_MPI_namespace::lp_reduce, Eigen::Matrix, double, nullptr>' requested here return lp_reduce(global_parameters, local_parameters, real_data, ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/functor/map_rect_reduce.hpp:47:12: note: in instantiation of function template specialization 'model_negBinomial_MPI_namespace::lp_reduce_functor__::operator(), Eigen::Matrix, double, nullptr>' requested here return F()(shared_params, job_specific_params, x_r, x_i, msgs).transpose(); ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/rev/functor/map_rect_concurrent.hpp:41:23: note: in instantiation of member function 'stan::math::internal::map_rect_reduce::operator()' requested here job_output[i] = ReduceF()(shared_params_dbl, value_of(job_params[i]), ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/functor/map_rect.hpp:183:20: note: in instantiation of function template specialization 'stan::math::internal::map_rect_concurrent<1, model_negBinomial_MPI_namespace::lp_reduce_functor__, const Eigen::Map> &, double, nullptr>' requested here return internal::map_rect_concurrent>, double, nullptr>' requested here stan::math::map_rect<1, lp_reduce_functor__>( ^ ./stanExports_negBinomial_MPI.h:1849:12: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all) return log_prob_impl(params_r, params_i, pstream); ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/stan/services/util/initialize.hpp:129:33: note: in instantiation of function template specialization 'model_negBinomial_MPI_namespace::model_negBinomial_MPI::log_prob' requested here log_prob = model.template log_prob(unconstrained, ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:49:43: note: in instantiation of function template specialization 'stan::services::util::initialize, boost::random::linear_congruential_engine>>' requested here std::vector cont_vector = util::initialize( ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:481:45: note: in instantiation of function template specialization 'stan::services::diagnose::diagnose' requested here return_code = stan::services::diagnose::diagnose(model, ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:1215:11: note: in instantiation of function template specialization 'rstan::(anonymous namespace)::command, boost::random::linear_congruential_engine>>' requested here ret = command(args, model_, holder, names_oi_tidx_, ^ stanExports_negBinomial_MPI.cc:15:87: note: in instantiation of member function 'rstan::stan_fit, boost::random::linear_congruential_engine>>::call_sampler' requested here .method("call_sampler", &rstan::stan_fit ::call_sampler) ^ In file included from stanExports_negBinomial_MPI.cc:5: ./stanExports_negBinomial_MPI.h:438:15: warning: unused variable 'global_parameters' [-Wunused-variable] const auto& global_parameters = stan::math::to_ref(global_parameters_arg__); ^ ./stanExports_negBinomial_MPI.h:242:12: note: in instantiation of function template specialization 'model_negBinomial_MPI_namespace::lp_reduce, Eigen::Matrix, -1, 1>, double, nullptr>' requested here return lp_reduce(global_parameters, local_parameters, real_data, ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/rev/functor/map_rect_reduce.hpp:68:21: note: in instantiation of function template specialization 'model_negBinomial_MPI_namespace::lp_reduce_functor__::operator(), Eigen::Matrix, -1, 1>, double, nullptr>' requested here vector_v fx_v = F()(shared_params, job_specific_params_v, x_r, x_i, msgs); ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/rev/functor/map_rect_concurrent.hpp:41:23: note: in instantiation of member function 'stan::math::internal::map_rect_reduce>::operator()' requested here job_output[i] = ReduceF()(shared_params_dbl, value_of(job_params[i]), ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/functor/map_rect.hpp:183:20: note: in instantiation of function template specialization 'stan::math::internal::map_rect_concurrent<1, model_negBinomial_MPI_namespace::lp_reduce_functor__, const Eigen::Map> &, stan::math::var_value, nullptr>' requested here return internal::map_rect_concurrent>, stan::math::var_value, nullptr>' requested here stan::math::map_rect<1, lp_reduce_functor__>( ^ ./stanExports_negBinomial_MPI.h:1849:12: note: (skipping 2 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) return log_prob_impl(params_r, params_i, pstream); ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/stan/services/util/initialize.hpp:167:31: note: in instantiation of function template specialization 'stan::model::log_prob_grad' requested here log_prob = stan::model::log_prob_grad( ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:49:43: note: in instantiation of function template specialization 'stan::services::util::initialize, boost::random::linear_congruential_engine>>' requested here std::vector cont_vector = util::initialize( ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:481:45: note: in instantiation of function template specialization 'stan::services::diagnose::diagnose' requested here return_code = stan::services::diagnose::diagnose(model, ^ /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:1215:11: note: in instantiation of function template specialization 'rstan::(anonymous namespace)::command, boost::random::linear_congruential_engine>>' requested here ret = command(args, model_, holder, names_oi_tidx_, ^ stanExports_negBinomial_MPI.cc:15:87: note: in instantiation of member function 'rstan::stan_fit, boost::random::linear_congruential_engine>>::call_sampler' requested here .method("call_sampler", &rstan::stan_fit ::call_sampler) ^ 13 warnings generated. clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o ppcseq.so RcppExports.o stanExports_negBinomial_MPI.o -L/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/lib -ltbb -ltbbmalloc -L/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/lib/ -Wl,-rpath,/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/lib/ -ltbb -ltbbmalloc -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation ld: warning: ignoring duplicate libraries: '-ltbb', '-ltbbmalloc' installing to /Users/biocbuild/bbs-3.20-bioc/meat/ppcseq.buildbin-libdir/00LOCK-ppcseq/00new/ppcseq/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (ppcseq) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR ppcseq.buildbin-libdir/ppcseq/libs/ppcseq.so >>>>>>> >>>>>>> Paths before fix: ppcseq.buildbin-libdir/ppcseq/libs/ppcseq.so: ppcseq.so (compatibility version 0.0.0, current version 0.0.0) @rpath/libtbb.dylib (compatibility version 0.0.0, current version 0.0.0) @rpath/libtbbmalloc.dylib (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) >>>>>>> Fix with install_name_tool: install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgcc_s.1.1.dylib" "ppcseq.buildbin-libdir/ppcseq/libs/ppcseq.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "ppcseq.buildbin-libdir/ppcseq/libs/ppcseq.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "ppcseq.buildbin-libdir/ppcseq/libs/ppcseq.so" >>>>>>> Paths after fix: ppcseq.buildbin-libdir/ppcseq/libs/ppcseq.so: ppcseq.so (compatibility version 0.0.0, current version 0.0.0) @rpath/libtbb.dylib (compatibility version 0.0.0, current version 0.0.0) @rpath/libtbbmalloc.dylib (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)