############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf sccomp.buildbin-libdir && mkdir sccomp.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh sccomp_1.0.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R sccomp.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=sccomp.buildbin-libdir sccomp_1.0.0.tar.gz' >>>>>>> * installing *source* package ‘sccomp’ ... ** using staged installation DIAGNOSTIC(S) FROM PARSER: Info: Left-hand side of sampling statement (~) may contain a non-linear transform of a parameter or local variable. If it does, you need to include a target += statement with the log absolute determinant of the Jacobian of the transform. Left-hand-side of sampling statement: to_vector(alpha_intercept_slope) ~ normal(...) ** libs clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include' -I/usr/local/include -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -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/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:1: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Core:540: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:2: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/LU:47: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:3: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Cholesky:12: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Jacobi:29: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:3: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Cholesky:43: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/QR:15: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Householder:27: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/QR:48: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:5: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/SVD:48: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:6: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Geometry:58: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:7: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Eigenvalues:58: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Sparse:26: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/SparseCore:66: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Sparse:27: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/OrderingMethods:71: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Sparse:29: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/SparseCholesky:43: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Sparse:32: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/SparseQR:34: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Sparse:33: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/IterativeLinearSolvers:46: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:32: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/CholmodSupport:45: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:35: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:39: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/unsupported/Eigen/Polynomials:135: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:40: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:51: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ 18 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include' -I/usr/local/include -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -Wall -g -O2 -c stanExports_glm_multi_beta_binomial.cc -o stanExports_glm_multi_beta_binomial.o In file included from stanExports_glm_multi_beta_binomial.cc:5: In file included from ./stanExports_glm_multi_beta_binomial.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:1: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Core:540: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial.cc:5: In file included from ./stanExports_glm_multi_beta_binomial.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:2: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/LU:47: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial.cc:5: In file included from ./stanExports_glm_multi_beta_binomial.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:3: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Cholesky:12: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Jacobi:29: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial.cc:5: In file included from ./stanExports_glm_multi_beta_binomial.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:3: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Cholesky:43: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial.cc:5: In file included from ./stanExports_glm_multi_beta_binomial.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/QR:15: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Householder:27: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial.cc:5: In file included from ./stanExports_glm_multi_beta_binomial.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/QR:48: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial.cc:5: In file included from ./stanExports_glm_multi_beta_binomial.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:5: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/SVD:48: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial.cc:5: In file included from ./stanExports_glm_multi_beta_binomial.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:6: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Geometry:58: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial.cc:5: In file included from ./stanExports_glm_multi_beta_binomial.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:7: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Eigenvalues:58: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial.cc:5: In file included from ./stanExports_glm_multi_beta_binomial.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Sparse:26: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/SparseCore:66: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial.cc:5: In file included from ./stanExports_glm_multi_beta_binomial.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Sparse:27: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/OrderingMethods:71: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial.cc:5: In file included from ./stanExports_glm_multi_beta_binomial.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Sparse:29: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/SparseCholesky:43: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial.cc:5: In file included from ./stanExports_glm_multi_beta_binomial.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Sparse:32: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/SparseQR:34: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial.cc:5: In file included from ./stanExports_glm_multi_beta_binomial.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Sparse:33: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/IterativeLinearSolvers:46: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial.cc:5: In file included from ./stanExports_glm_multi_beta_binomial.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:22: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:32: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/CholmodSupport:45: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial.cc:5: In file included from ./stanExports_glm_multi_beta_binomial.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:22: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:35: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial.cc:5: In file included from ./stanExports_glm_multi_beta_binomial.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:22: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:39: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/unsupported/Eigen/Polynomials:135: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial.cc:5: In file included from ./stanExports_glm_multi_beta_binomial.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:22: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:40: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:51: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial.cc:5: In file included from ./stanExports_glm_multi_beta_binomial.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:35: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:283: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/prob/gaussian_dlm_obs_rng.hpp:138:7: warning: unused variable 'n' [-Wunused-variable] int n = G.rows(); // number of states ^ In file included from stanExports_glm_multi_beta_binomial.cc:5: In file included from ./stanExports_glm_multi_beta_binomial.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:35: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:17: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/columns_dot_self.hpp:8: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/dot_self.hpp:38:41: warning: all paths through this function will call itself [-Winfinite-recursion] inline static double square(double x) { return square(x); } ^ In file included from stanExports_glm_multi_beta_binomial.cc:5: In file included from ./stanExports_glm_multi_beta_binomial.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:35: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:70: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat/functor/integrate_ode_adams.hpp:5: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat/functor/cvodes_integrator.hpp:126:18: warning: unused variable 'coupled_size' [-Wunused-variable] const size_t coupled_size = cvodes_data.coupled_ode_.size(); ^ In file included from stanExports_glm_multi_beta_binomial.cc:5: In file included from ./stanExports_glm_multi_beta_binomial.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:35: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:6: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:46: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:14:13: warning: unused function 'set_zero_all_adjoints' [-Wunused-function] static void set_zero_all_adjoints() { ^ In file included from stanExports_glm_multi_beta_binomial.cc:5: In file included from ./stanExports_glm_multi_beta_binomial.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:35: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:6: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:47: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints_nested.hpp:17:13: warning: 'static' function 'set_zero_all_adjoints_nested' declared in header file should be declared 'static inline' [-Wunneeded-internal-declaration] static void set_zero_all_adjoints_nested() { ^ In file included from stanExports_glm_multi_beta_binomial.cc:5: In file included from ./stanExports_glm_multi_beta_binomial.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:35: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:278: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_log.hpp:5: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_lpmf.hpp:60:9: warning: unused type alias 'T_partials_vec' [-Wunused-local-typedef] using T_partials_vec = typename Eigen::Matrix; ^ In file included from stanExports_glm_multi_beta_binomial.cc:5: In file included from ./stanExports_glm_multi_beta_binomial.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:35: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:328: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_log.hpp:5: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_lpmf.hpp:52:9: warning: unused type alias 'T_alpha_val' [-Wunused-local-typedef] using T_alpha_val = typename std::conditional_t< ^ In file included from stanExports_glm_multi_beta_binomial.cc:5: In file included from ./stanExports_glm_multi_beta_binomial.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:35: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:51: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:27:11: warning: unused type alias 'idx_t' [-Wunused-local-typedef] using idx_t = typename index_type::type; ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:64:11: warning: unused type alias 'idx_t' [-Wunused-local-typedef] using idx_t = typename index_type::type; ^ In file included from stanExports_glm_multi_beta_binomial.cc:5: ./stanExports_glm_multi_beta_binomial.h:573:24: warning: unused typedef 'local_scalar_t__' [-Wunused-local-typedef] typedef double local_scalar_t__; ^ 28 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include' -I/usr/local/include -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -Wall -g -O2 -c stanExports_glm_multi_beta_binomial_generate_date.cc -o stanExports_glm_multi_beta_binomial_generate_date.o In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:1: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Core:540: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:2: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/LU:47: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:3: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Cholesky:12: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Jacobi:29: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:3: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Cholesky:43: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/QR:15: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Householder:27: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/QR:48: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:5: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/SVD:48: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:6: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Geometry:58: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:7: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Eigenvalues:58: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Sparse:26: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/SparseCore:66: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Sparse:27: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/OrderingMethods:71: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Sparse:29: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/SparseCholesky:43: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Sparse:32: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/SparseQR:34: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Sparse:33: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/IterativeLinearSolvers:46: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:22: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:32: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/CholmodSupport:45: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:22: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:35: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:22: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:39: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/unsupported/Eigen/Polynomials:135: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:22: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:40: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:51: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:35: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:283: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/prob/gaussian_dlm_obs_rng.hpp:138:7: warning: unused variable 'n' [-Wunused-variable] int n = G.rows(); // number of states ^ In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:35: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:17: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/columns_dot_self.hpp:8: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/dot_self.hpp:38:41: warning: all paths through this function will call itself [-Winfinite-recursion] inline static double square(double x) { return square(x); } ^ In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:35: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:70: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat/functor/integrate_ode_adams.hpp:5: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat/functor/cvodes_integrator.hpp:126:18: warning: unused variable 'coupled_size' [-Wunused-variable] const size_t coupled_size = cvodes_data.coupled_ode_.size(); ^ In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:35: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:6: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:46: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:14:13: warning: unused function 'set_zero_all_adjoints' [-Wunused-function] static void set_zero_all_adjoints() { ^ In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:35: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:6: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:47: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints_nested.hpp:17:13: warning: 'static' function 'set_zero_all_adjoints_nested' declared in header file should be declared 'static inline' [-Wunneeded-internal-declaration] static void set_zero_all_adjoints_nested() { ^ In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:35: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:278: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_log.hpp:5: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_lpmf.hpp:60:9: warning: unused type alias 'T_partials_vec' [-Wunused-local-typedef] using T_partials_vec = typename Eigen::Matrix; ^ In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:35: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:328: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_log.hpp:5: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_lpmf.hpp:52:9: warning: unused type alias 'T_alpha_val' [-Wunused-local-typedef] using T_alpha_val = typename std::conditional_t< ^ In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_generate_date.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:35: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:51: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:27:11: warning: unused type alias 'idx_t' [-Wunused-local-typedef] using idx_t = typename index_type::type; ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:64:11: warning: unused type alias 'idx_t' [-Wunused-local-typedef] using idx_t = typename index_type::type; ^ In file included from stanExports_glm_multi_beta_binomial_generate_date.cc:5: ./stanExports_glm_multi_beta_binomial_generate_date.h:167:24: warning: unused typedef 'local_scalar_t__' [-Wunused-local-typedef] typedef double local_scalar_t__; ^ 28 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include' -I/usr/local/include -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -Wall -g -O2 -c stanExports_glm_multi_beta_binomial_simulate_data.cc -o stanExports_glm_multi_beta_binomial_simulate_data.o In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:1: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Core:540: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:2: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/LU:47: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:3: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Cholesky:12: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Jacobi:29: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:3: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Cholesky:43: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/QR:15: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Householder:27: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/QR:48: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:5: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/SVD:48: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:6: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Geometry:58: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:7: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Eigenvalues:58: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Sparse:26: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/SparseCore:66: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Sparse:27: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/OrderingMethods:71: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Sparse:29: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/SparseCholesky:43: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Sparse:32: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/SparseQR:34: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Sparse:33: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/IterativeLinearSolvers:46: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:22: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:32: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/CholmodSupport:45: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:22: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:35: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:22: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:39: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/unsupported/Eigen/Polynomials:135: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:22: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:40: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:51: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:35: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:283: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/prob/gaussian_dlm_obs_rng.hpp:138:7: warning: unused variable 'n' [-Wunused-variable] int n = G.rows(); // number of states ^ In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:35: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:17: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/columns_dot_self.hpp:8: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/dot_self.hpp:38:41: warning: all paths through this function will call itself [-Winfinite-recursion] inline static double square(double x) { return square(x); } ^ In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:35: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:70: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat/functor/integrate_ode_adams.hpp:5: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat/functor/cvodes_integrator.hpp:126:18: warning: unused variable 'coupled_size' [-Wunused-variable] const size_t coupled_size = cvodes_data.coupled_ode_.size(); ^ In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:35: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:6: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:46: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:14:13: warning: unused function 'set_zero_all_adjoints' [-Wunused-function] static void set_zero_all_adjoints() { ^ In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:35: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:6: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:47: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints_nested.hpp:17:13: warning: 'static' function 'set_zero_all_adjoints_nested' declared in header file should be declared 'static inline' [-Wunneeded-internal-declaration] static void set_zero_all_adjoints_nested() { ^ In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:35: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:278: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_log.hpp:5: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_lpmf.hpp:60:9: warning: unused type alias 'T_partials_vec' [-Wunused-local-typedef] using T_partials_vec = typename Eigen::Matrix; ^ In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:35: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:328: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_log.hpp:5: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_lpmf.hpp:52:9: warning: unused type alias 'T_alpha_val' [-Wunused-local-typedef] using T_alpha_val = typename std::conditional_t< ^ In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: In file included from ./stanExports_glm_multi_beta_binomial_simulate_data.h:20: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:35: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:51: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:27:11: warning: unused type alias 'idx_t' [-Wunused-local-typedef] using idx_t = typename index_type::type; ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:64:11: warning: unused type alias 'idx_t' [-Wunused-local-typedef] using idx_t = typename index_type::type; ^ In file included from stanExports_glm_multi_beta_binomial_simulate_data.cc:5: ./stanExports_glm_multi_beta_binomial_simulate_data.h:187:24: warning: unused typedef 'local_scalar_t__' [-Wunused-local-typedef] typedef double local_scalar_t__; ^ 28 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o sccomp.so RcppExports.o stanExports_glm_multi_beta_binomial.o stanExports_glm_multi_beta_binomial_generate_date.o stanExports_glm_multi_beta_binomial_simulate_data.o -L/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/lib/ -Wl,-rpath,/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/lib/ -ltbb -ltbbmalloc -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.15-bioc/meat/sccomp.buildbin-libdir/00LOCK-sccomp/00new/sccomp/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading DIAGNOSTIC(S) FROM PARSER: Info: Left-hand side of sampling statement (~) may contain a non-linear transform of a parameter or local variable. If it does, you need to include a target += statement with the log absolute determinant of the Jacobian of the transform. Left-hand-side of sampling statement: to_vector(alpha_intercept_slope) ~ normal(...) ** 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 (sccomp) >>>>>>> >>>>>>> FIXING LINKS FOR sccomp.buildbin-libdir/sccomp/libs/sccomp.so >>>>>>> install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgcc_s.1.dylib" "sccomp.buildbin-libdir/sccomp/libs/sccomp.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgfortran.5.dylib" "sccomp.buildbin-libdir/sccomp/libs/sccomp.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libquadmath.0.dylib" "sccomp.buildbin-libdir/sccomp/libs/sccomp.so"