##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf IgGeneUsage.buildbin-libdir && mkdir IgGeneUsage.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh IgGeneUsage_1.14.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R IgGeneUsage.buildbin-libdir
###
##############################################################################
##############################################################################
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=IgGeneUsage.buildbin-libdir IgGeneUsage_1.14.0.tar.gz'
>>>>>>>
* installing *source* package ‘IgGeneUsage’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++17
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -D_HAS_AUTO_PTR_ETC=0 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include' -I/opt/R/arm64/include -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -D_HAS_AUTO_PTR_ETC=0 -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Core:540:
/Library/Frameworks/R.framework/Versions/4.3-arm64/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/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Dense:2:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/LU:47:
/Library/Frameworks/R.framework/Versions/4.3-arm64/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/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Cholesky:12:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Jacobi:29:
/Library/Frameworks/R.framework/Versions/4.3-arm64/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/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Cholesky:43:
/Library/Frameworks/R.framework/Versions/4.3-arm64/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/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Dense:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/QR:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Householder:27:
/Library/Frameworks/R.framework/Versions/4.3-arm64/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/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Dense:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/QR:48:
/Library/Frameworks/R.framework/Versions/4.3-arm64/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/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Dense:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/SVD:48:
/Library/Frameworks/R.framework/Versions/4.3-arm64/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/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Dense:6:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Geometry:58:
/Library/Frameworks/R.framework/Versions/4.3-arm64/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/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Dense:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Eigenvalues:58:
/Library/Frameworks/R.framework/Versions/4.3-arm64/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/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:66:
/Library/Frameworks/R.framework/Versions/4.3-arm64/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/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:27:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/OrderingMethods:71:
/Library/Frameworks/R.framework/Versions/4.3-arm64/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/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/SparseCholesky:43:
/Library/Frameworks/R.framework/Versions/4.3-arm64/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/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:32:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/SparseQR:34:
/Library/Frameworks/R.framework/Versions/4.3-arm64/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/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:33:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
/Library/Frameworks/R.framework/Versions/4.3-arm64/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/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:32:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/CholmodSupport:45:
/Library/Frameworks/R.framework/Versions/4.3-arm64/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/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34:
/Library/Frameworks/R.framework/Versions/4.3-arm64/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/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:39:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/Polynomials:135:
/Library/Frameworks/R.framework/Versions/4.3-arm64/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/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:40:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:51:
/Library/Frameworks/R.framework/Versions/4.3-arm64/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++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -D_HAS_AUTO_PTR_ETC=0 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include' -I/opt/R/arm64/include -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -D_HAS_AUTO_PTR_ETC=0 -fPIC -falign-functions=64 -Wall -g -O2 -c stanExports_zibb.cc -o stanExports_zibb.o
In file included from stanExports_zibb.cc:5:
In file included from ./stanExports_zibb.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/../../fun/Eigen.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Core:540:
/Library/Frameworks/R.framework/Versions/4.3-arm64/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_zibb.cc:5:
In file included from ./stanExports_zibb.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/../../fun/Eigen.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Dense:2:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/LU:47:
/Library/Frameworks/R.framework/Versions/4.3-arm64/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_zibb.cc:5:
In file included from ./stanExports_zibb.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/../../fun/Eigen.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Cholesky:12:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Jacobi:29:
/Library/Frameworks/R.framework/Versions/4.3-arm64/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_zibb.cc:5:
In file included from ./stanExports_zibb.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/../../fun/Eigen.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Cholesky:43:
/Library/Frameworks/R.framework/Versions/4.3-arm64/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_zibb.cc:5:
In file included from ./stanExports_zibb.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/../../fun/Eigen.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Dense:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/QR:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Householder:27:
/Library/Frameworks/R.framework/Versions/4.3-arm64/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_zibb.cc:5:
In file included from ./stanExports_zibb.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/../../fun/Eigen.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Dense:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/QR:48:
/Library/Frameworks/R.framework/Versions/4.3-arm64/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_zibb.cc:5:
In file included from ./stanExports_zibb.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/../../fun/Eigen.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Dense:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/SVD:48:
/Library/Frameworks/R.framework/Versions/4.3-arm64/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_zibb.cc:5:
In file included from ./stanExports_zibb.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/../../fun/Eigen.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Dense:6:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Geometry:58:
/Library/Frameworks/R.framework/Versions/4.3-arm64/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_zibb.cc:5:
In file included from ./stanExports_zibb.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/../../fun/Eigen.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Dense:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Eigenvalues:58:
/Library/Frameworks/R.framework/Versions/4.3-arm64/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_zibb.cc:5:
In file included from ./stanExports_zibb.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/../../fun/Eigen.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:66:
/Library/Frameworks/R.framework/Versions/4.3-arm64/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_zibb.cc:5:
In file included from ./stanExports_zibb.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/../../fun/Eigen.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:27:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/OrderingMethods:71:
/Library/Frameworks/R.framework/Versions/4.3-arm64/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_zibb.cc:5:
In file included from ./stanExports_zibb.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/../../fun/Eigen.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/SparseCholesky:43:
/Library/Frameworks/R.framework/Versions/4.3-arm64/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_zibb.cc:5:
In file included from ./stanExports_zibb.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/../../fun/Eigen.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:32:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/SparseQR:34:
/Library/Frameworks/R.framework/Versions/4.3-arm64/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_zibb.cc:5:
In file included from ./stanExports_zibb.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/../../fun/Eigen.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:33:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
/Library/Frameworks/R.framework/Versions/4.3-arm64/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_zibb.cc:5:
In file included from ./stanExports_zibb.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:32:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/CholmodSupport:45:
/Library/Frameworks/R.framework/Versions/4.3-arm64/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_zibb.cc:5:
In file included from ./stanExports_zibb.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34:
/Library/Frameworks/R.framework/Versions/4.3-arm64/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_zibb.cc:5:
In file included from ./stanExports_zibb.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:39:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/Polynomials:135:
/Library/Frameworks/R.framework/Versions/4.3-arm64/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_zibb.cc:5:
In file included from ./stanExports_zibb.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:40:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:51:
/Library/Frameworks/R.framework/Versions/4.3-arm64/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_zibb.cc:5:
In file included from ./stanExports_zibb.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev.hpp:8:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:28:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev/core/operator_addition.hpp:6:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/err/check_matching_dims.hpp:33:8: warning: unused variable 'error' [-Wunused-variable]
bool error = false;
^
In file included from stanExports_zibb.cc:5:
In file included from ./stanExports_zibb.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev.hpp:8:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:54:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev/core/profiling.hpp:9:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/err.hpp:50:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/err/hmm_check.hpp:33:7: warning: unused variable 'n_transitions' [-Wunused-variable]
int n_transitions = log_omegas.cols() - 1;
^
In file included from stanExports_zibb.cc:5:
In file included from ./stanExports_zibb.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev/fun.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:118:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/gp_matern52_cov.hpp:275:10: warning: unused variable 'neg_root_5' [-Wunused-variable]
double neg_root_5 = -root_5;
^
In file included from stanExports_zibb.cc:5:
In file included from ./stanExports_zibb.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev/fun.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:183:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/log_mix.hpp:86:13: warning: unused variable 'N' [-Wunused-variable]
const int N = stan::math::size(theta);
^
In file included from stanExports_zibb.cc:5:
In file included from ./stanExports_zibb.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim.hpp:16:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/prob.hpp:87:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/prob/double_exponential_cdf.hpp:82:10: warning: unused variable 'N' [-Wunused-variable]
size_t N = max_size(y, mu, sigma);
^
In file included from stanExports_zibb.cc:5:
In file included from ./stanExports_zibb.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim.hpp:16:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/prob.hpp:128:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/prob/gaussian_dlm_obs_rng.hpp:98:7: warning: unused variable 'n' [-Wunused-variable]
int n = G.rows(); // number of states
^
In file included from stanExports_zibb.cc:5:
In file included from ./stanExports_zibb.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim.hpp:16:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/prob.hpp:139:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/prob/hmm_marginal.hpp:26:13: warning: unused variable 'n_states' [-Wunused-variable]
const int n_states = omegas.rows();
^
In file included from stanExports_zibb.cc:5:
In file included from ./stanExports_zibb.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim.hpp:16:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/prob.hpp:315:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/prob/std_normal_rng.hpp:23:22: warning: unused variable 'function' [-Wunused-variable]
static const char* function = "std_normal_rng";
^
In file included from stanExports_zibb.cc:5:
In file included from ./stanExports_zibb.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim.hpp:16:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/prob.hpp:335:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/prob/von_mises_cdf.hpp:72:10: warning: unused variable 'ck' [-Wunused-variable]
double ck = 50;
^
In file included from stanExports_zibb.cc:5:
In file included from ./stanExports_zibb.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:1238:9: warning: variable 'ret' set but not used [-Wunused-but-set-variable]
int ret = stan::services::error_codes::CONFIG;
^
In file included from stanExports_zibb.cc:5:
In file included from ./stanExports_zibb.h:22:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/indexing.hpp:9:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/indexing/rvalue.hpp:610:13: warning: unused variable 'cols' [-Wunused-variable]
const int cols = rvalue_index_size(idxs.tail_.head_, x_ref.cols());
^
In file included from stanExports_zibb.cc:5:
In file included from ./stanExports_zibb.h:22:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/indexing.hpp:10:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/indexing/rvalue_varmat.hpp:241:22: warning: unused variable 'x_cols' [-Wunused-variable]
const Eigen::Index x_cols = x.cols();
^
In file included from stanExports_zibb.cc:5:
In file included from ./stanExports_zibb.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev.hpp:8:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:29:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev/core/operator_divide_equal.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev/core/operator_division.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev/core/operator_multiplication.hpp:7:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev/core/operator_subtraction.hpp:88:43: warning: lambda capture 'b' is not used [-Wunused-lambda-capture]
[avi = a.vi_, b](const auto& vi) mutable {
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev/core/operator_minus_equal.hpp:24:16: note: in instantiation of function template specialization 'stan::math::operator-<double, nullptr>' requested here
vi_ = (*this - b).vi_;
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/core/complex_base.hpp:136:9: note: in instantiation of member function 'stan::math::var_value<double>::operator-=' requested here
re_ -= x;
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/core/operator_subtraction.hpp:24:5: note: in instantiation of function template specialization 'stan::math::complex_base<stan::math::var_value<double>>::operator-=<int>' requested here
y -= rhs;
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/core/operator_subtraction.hpp:55:20: note: in instantiation of function template specialization 'stan::math::internal::complex_subtract<std::complex<stan::math::var>, int>' requested here
return internal::complex_subtract(x, y);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/acosh.hpp:105:31: note: in instantiation of function template specialization 'stan::math::operator-<stan::math::var_value<double>, int>' requested here
auto y = log(z + sqrt(z * z - 1));
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev/fun/acosh.hpp:94:32: note: in instantiation of function template specialization 'stan::math::internal::complex_acosh<stan::math::var_value<double>>' requested here
return stan::math::internal::complex_acosh(z);
^
In file included from stanExports_zibb.cc:5:
In file included from ./stanExports_zibb.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev.hpp:8:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:28:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev/core/operator_addition.hpp:84:43: warning: lambda capture 'b' is not used [-Wunused-lambda-capture]
[avi = a.vi_, b](const auto& vi) mutable {
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev/fun/grad_inc_beta.hpp:45:43: note: in instantiation of function template specialization 'stan::math::operator+<int, nullptr>' requested here
grad_2F1(dF1, dF2, a + b, var(1.0), a + 1, z);
^
In file included from stanExports_zibb.cc:5:
In file included from ./stanExports_zibb.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev.hpp:8:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:28:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev/core/operator_addition.hpp:84:43: warning: lambda capture 'b' is not used [-Wunused-lambda-capture]
[avi = a.vi_, b](const auto& vi) mutable {
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/trigamma.hpp:63:31: note: in instantiation of function template specialization 'stan::math::operator+<double, nullptr>' requested here
value = -trigamma_impl(-x + 1.0) + square(pi() / sin(-pi() * x));
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev/fun/trigamma.hpp:23:44: note: in instantiation of function template specialization 'stan::math::trigamma_impl<stan::math::var_value<double>>' requested here
inline var trigamma(const var& u) { return trigamma_impl(u); }
^
In file included from stanExports_zibb.cc:5:
In file included from ./stanExports_zibb.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev.hpp:8:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:29:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev/core/operator_divide_equal.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev/core/operator_division.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev/core/operator_multiplication.hpp:7:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev/core/operator_subtraction.hpp:113:43: warning: lambda capture 'a' is not used [-Wunused-lambda-capture]
[bvi = b.vi_, a](const auto& vi) mutable {
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/ub_constrain.hpp:77:13: note: in instantiation of function template specialization 'stan::math::operator-<int, nullptr>' requested here
return ub - exp(x);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/lub_constrain.hpp:107:12: note: in instantiation of function template specialization 'stan::math::ub_constrain<stan::math::var_value<double>, int>' requested here
return ub_constrain(x, ub, lp);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/io/reader.hpp:748:24: note: in instantiation of function template specialization 'stan::math::lub_constrain<stan::math::var_value<double>, int, int, stan::math::var_value<double>>' requested here
return stan::math::lub_constrain(scalar(), lb, ub, lp);
^
./stanExports_zibb.h:496:26: note: in instantiation of function template specialization 'stan::io::reader<stan::math::var_value<double>>::scalar_lub_constrain<int, int>' requested here
z = in__.scalar_lub_constrain(0, 1, lp__);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:40:36: note: in instantiation of function template specialization 'model_zibb_namespace::model_zibb::log_prob<true, true, stan::math::var_value<double>>' requested here
var adLogProb = model.template log_prob<propto, jacobian_adjust_transform>(
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/services/util/initialize.hpp:166:31: note: in instantiation of function template specialization 'stan::model::log_prob_grad<true, true, model_zibb_namespace::model_zibb>' requested here
log_prob = stan::model::log_prob_grad<true, Jacobian>(
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:49:43: note: in instantiation of function template specialization 'stan::services::util::initialize<true, model_zibb_namespace::model_zibb, boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399>>>' requested here
std::vector<double> cont_vector = util::initialize(
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:467:45: note: in instantiation of function template specialization 'stan::services::diagnose::diagnose<model_zibb_namespace::model_zibb>' requested here
return_code = stan::services::diagnose::diagnose(model,
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:1201:11: note: in instantiation of function template specialization 'rstan::(anonymous namespace)::command<model_zibb_namespace::model_zibb, boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399>>>' requested here
ret = command(args, model_, holder, names_oi_tidx_,
^
stanExports_zibb.cc:15:87: note: in instantiation of member function 'rstan::stan_fit<model_zibb_namespace::model_zibb, boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399>>>::call_sampler' requested here
.method("call_sampler", &rstan::stan_fit<stan_model, boost::random::ecuyer1988> ::call_sampler)
^
In file included from stanExports_zibb.cc:5:
In file included from ./stanExports_zibb.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev.hpp:8:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:29:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev/core/operator_divide_equal.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev/core/operator_division.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev/core/operator_multiplication.hpp:7:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev/core/operator_subtraction.hpp:113:43: warning: lambda capture 'a' is not used [-Wunused-lambda-capture]
[bvi = b.vi_, a](const auto& vi) mutable {
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/lub_constrain.hpp:115:24: note: in instantiation of function template specialization 'stan::math::operator-<double, nullptr>' requested here
lp += log(ub - lb) - x - 2 * log1p(exp_minus_x);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/io/reader.hpp:748:24: note: in instantiation of function template specialization 'stan::math::lub_constrain<stan::math::var_value<double>, int, int, stan::math::var_value<double>>' requested here
return stan::math::lub_constrain(scalar(), lb, ub, lp);
^
./stanExports_zibb.h:496:26: note: in instantiation of function template specialization 'stan::io::reader<stan::math::var_value<double>>::scalar_lub_constrain<int, int>' requested here
z = in__.scalar_lub_constrain(0, 1, lp__);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:40:36: note: in instantiation of function template specialization 'model_zibb_namespace::model_zibb::log_prob<true, true, stan::math::var_value<double>>' requested here
var adLogProb = model.template log_prob<propto, jacobian_adjust_transform>(
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/services/util/initialize.hpp:166:31: note: in instantiation of function template specialization 'stan::model::log_prob_grad<true, true, model_zibb_namespace::model_zibb>' requested here
log_prob = stan::model::log_prob_grad<true, Jacobian>(
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:49:43: note: in instantiation of function template specialization 'stan::services::util::initialize<true, model_zibb_namespace::model_zibb, boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399>>>' requested here
std::vector<double> cont_vector = util::initialize(
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:467:45: note: in instantiation of function template specialization 'stan::services::diagnose::diagnose<model_zibb_namespace::model_zibb>' requested here
return_code = stan::services::diagnose::diagnose(model,
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:1201:11: note: in instantiation of function template specialization 'rstan::(anonymous namespace)::command<model_zibb_namespace::model_zibb, boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399>>>' requested here
ret = command(args, model_, holder, names_oi_tidx_,
^
stanExports_zibb.cc:15:87: note: in instantiation of member function 'rstan::stan_fit<model_zibb_namespace::model_zibb, boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399>>>::call_sampler' requested here
.method("call_sampler", &rstan::stan_fit<stan_model, boost::random::ecuyer1988> ::call_sampler)
^
In file included from stanExports_zibb.cc:5:
In file included from ./stanExports_zibb.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev.hpp:8:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:52:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev/core/precomputed_gradients.hpp:83:59: warning: lambda capture 'this' is not used [-Wunused-lambda-capture]
container_operands_(index_apply<N_containers>([&, this](auto... Is) {
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev/functor/operands_and_partials.hpp:167:16: note: in instantiation of function template specialization 'stan::math::precomputed_gradients_vari_template<>::precomputed_gradients_vari_template<>' requested here
return new precomputed_gradients_vari_template<
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/prob/bernoulli_lpmf.hpp:110:23: note: in instantiation of member function 'stan::math::operands_and_partials<const stan::math::var_value<double> &, double, double, double, double, stan::math::var_value<double>>::build' requested here
return ops_partials.build(logp);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/prob/bernoulli_lpmf.hpp:115:10: note: in instantiation of function template specialization 'stan::math::bernoulli_lpmf<false, int, stan::math::var_value<double>, nullptr>' requested here
return bernoulli_lpmf<false>(n, theta);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/prob/bernoulli_log.hpp:23:10: note: in instantiation of function template specialization 'stan::math::bernoulli_lpmf<int, stan::math::var_value<double>>' requested here
return bernoulli_lpmf<T_y, T_prob>(n, theta);
^
./stanExports_zibb.h:57:82: note: in instantiation of function template specialization 'stan::math::bernoulli_log<int, stan::math::var_value<double>>' requested here
return stan::math::promote_scalar<fun_return_scalar_t__>(log_sum_exp(bernoulli_log(1, zi), (bernoulli_log(0, zi) + beta_binomial_log(0, trials, a, b))));
^
./stanExports_zibb.h:75:12: note: (skipping 3 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
return zibb_lpmf<false>(y,trials,a,b,zi, pstream__);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/services/util/initialize.hpp:166:31: note: in instantiation of function template specialization 'stan::model::log_prob_grad<true, true, model_zibb_namespace::model_zibb>' requested here
log_prob = stan::model::log_prob_grad<true, Jacobian>(
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:49:43: note: in instantiation of function template specialization 'stan::services::util::initialize<true, model_zibb_namespace::model_zibb, boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399>>>' requested here
std::vector<double> cont_vector = util::initialize(
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:467:45: note: in instantiation of function template specialization 'stan::services::diagnose::diagnose<model_zibb_namespace::model_zibb>' requested here
return_code = stan::services::diagnose::diagnose(model,
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:1201:11: note: in instantiation of function template specialization 'rstan::(anonymous namespace)::command<model_zibb_namespace::model_zibb, boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399>>>' requested here
ret = command(args, model_, holder, names_oi_tidx_,
^
stanExports_zibb.cc:15:87: note: in instantiation of member function 'rstan::stan_fit<model_zibb_namespace::model_zibb, boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399>>>::call_sampler' requested here
.method("call_sampler", &rstan::stan_fit<stan_model, boost::random::ecuyer1988> ::call_sampler)
^
In file included from stanExports_zibb.cc:5:
In file included from ./stanExports_zibb.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev.hpp:8:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:52:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev/core/precomputed_gradients.hpp:86:60: warning: lambda capture 'this' is not used [-Wunused-lambda-capture]
container_gradients_(index_apply<N_containers>([&, this](auto... Is) {
^
In file included from stanExports_zibb.cc:5:
In file included from ./stanExports_zibb.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev.hpp:8:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:59:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:14:13: warning: 'static' function 'set_zero_all_adjoints' declared in header file should be declared 'static inline' [-Wunneeded-internal-declaration]
static void set_zero_all_adjoints() {
^
In file included from stanExports_zibb.cc:5:
In file included from ./stanExports_zibb.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev/fun.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:110:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/generalized_inverse.hpp:34:9: warning: unused type alias 'value_t' [-Wunused-local-typedef]
using value_t = value_type_t<EigMat>;
^
In file included from stanExports_zibb.cc:5:
In file included from ./stanExports_zibb.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev/fun.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:319:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/tail.hpp:46:9: warning: unused type alias 'idx_t' [-Wunused-local-typedef]
using idx_t = index_type_t<std::vector<T>>;
^
In file included from stanExports_zibb.cc:5:
In file included from ./stanExports_zibb.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev/fun.hpp:32:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev/fun/cholesky_decompose.hpp:83:11: warning: unused type alias 'Block_' [-Wunused-local-typedef]
using Block_ = Eigen::Block<Eigen::MatrixXd>;
^
In file included from stanExports_zibb.cc:5:
In file included from ./stanExports_zibb.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev/fun.hpp:34:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev/fun/cholesky_factor_constrain.hpp:32:9: warning: unused type alias 'T_scalar' [-Wunused-local-typedef]
using T_scalar = value_type_t<T>;
^
In file included from stanExports_zibb.cc:5:
In file included from ./stanExports_zibb.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev/fun.hpp:71:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev/fun/generalized_inverse.hpp:64:9: warning: unused type alias 'value_t' [-Wunused-local-typedef]
using value_t = value_type_t<VarMat>;
^
In file included from stanExports_zibb.cc:5:
In file included from ./stanExports_zibb.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim.hpp:16:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/prob.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/prob/bernoulli_logit_glm_log.hpp:5:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/prob/bernoulli_logit_glm_lpmf.hpp:59:9: warning: unused type alias 'T_y_val' [-Wunused-local-typedef]
using T_y_val =
^
In file included from stanExports_zibb.cc:5:
In file included from ./stanExports_zibb.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim.hpp:16:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/prob.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/prob/beta_log.hpp:5:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/prob/beta_lpdf.hpp:50:9: warning: unused type alias 'T_partials_matrix' [-Wunused-local-typedef]
using T_partials_matrix = Eigen::Matrix<T_partials_return, Eigen::Dynamic, 1>;
^
In file included from stanExports_zibb.cc:5:
In file included from ./stanExports_zibb.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim.hpp:16:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/prob.hpp:37:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/prob/beta_proportion_log.hpp:5:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/prob/beta_proportion_lpdf.hpp:55:9: warning: unused type alias 'T_partials_array' [-Wunused-local-typedef]
using T_partials_array = Eigen::Array<T_partials_return, Eigen::Dynamic, 1>;
^
In file included from stanExports_zibb.cc:5:
In file included from ./stanExports_zibb.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim.hpp:16:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/prob.hpp:63:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/prob/cauchy_log.hpp:5:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/prob/cauchy_lpdf.hpp:45:9: warning: unused type alias 'T_partials_array' [-Wunused-local-typedef]
using T_partials_array = Eigen::Array<T_partials_return, Eigen::Dynamic, 1>;
^
In file included from stanExports_zibb.cc:5:
In file included from ./stanExports_zibb.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim.hpp:16:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/prob.hpp:74:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/prob/dirichlet_log.hpp:5:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/prob/dirichlet_lpdf.hpp:60:9: warning: unused type alias 'T_partials_vec' [-Wunused-local-typedef]
using T_partials_vec = typename Eigen::Matrix<T_partials_return, -1, 1>;
^
In file included from stanExports_zibb.cc:5:
In file included from ./stanExports_zibb.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim.hpp:16:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/prob.hpp:91:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/prob/double_exponential_log.hpp:5:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/prob/double_exponential_lpdf.hpp:44:9: warning: unused type alias 'T_partials_array' [-Wunused-local-typedef]
using T_partials_array = Eigen::Array<T_partials_return, Eigen::Dynamic, 1>;
^
In file included from stanExports_zibb.cc:5:
In file included from ./stanExports_zibb.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim.hpp:16:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/prob.hpp:111:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/prob/frechet_cdf.hpp:30:9: warning: unused type alias 'T_partials_array' [-Wunused-local-typedef]
using T_partials_array = Eigen::Array<T_partials_return, Eigen::Dynamic, 1>;
^
In file included from stanExports_zibb.cc:5:
In file included from ./stanExports_zibb.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim.hpp:16:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/prob.hpp:245:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/prob/ordered_logistic_log.hpp:5:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/prob/ordered_logistic_lpmf.hpp:76:9: warning: unused type alias 'T_partials_array' [-Wunused-local-typedef]
using T_partials_array = Eigen::Array<T_partials_return, -1, 1>;
^
In file included from stanExports_zibb.cc:5:
In file included from ./stanExports_zibb.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/rev.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim.hpp:16:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/prob.hpp:277:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/prob/poisson_log_glm_log.hpp:5:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/prob/poisson_log_glm_lpmf.hpp:62:9: warning: unused type alias 'T_alpha_val' [-Wunused-local-typedef]
using T_alpha_val = typename std::conditional_t<
^
In file included from stanExports_zibb.cc:5:
In file included from ./stanExports_zibb.h:22:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/indexing.hpp:8:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/model/indexing/lvalue_varmat.hpp:349:9: warning: unused type alias 'pair_type' [-Wunused-local-typedef]
using pair_type = std::pair<int, arena_vec>;
^
In file included from stanExports_zibb.cc:5:
./stanExports_zibb.h:266:24: warning: unused typedef 'local_scalar_t__' [-Wunused-local-typedef]
typedef double local_scalar_t__;
^
54 warnings generated.
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o IgGeneUsage.so RcppExports.o stanExports_zibb.o -L/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/lib/ -Wl,-rpath,/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/lib/ -ltbb -ltbbmalloc -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/IgGeneUsage.buildbin-libdir/00LOCK-IgGeneUsage/00new/IgGeneUsage/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (IgGeneUsage)
>>>>>>>
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR IgGeneUsage.buildbin-libdir/IgGeneUsage/libs/IgGeneUsage.so
>>>>>>>
>>>>>>> Paths before fix:
IgGeneUsage.buildbin-libdir/IgGeneUsage/libs/IgGeneUsage.so:
IgGeneUsage.so (compatibility version 0.0.0, current version 0.0.0)
@rpath/libtbb.dylib (compatibility version 0.0.0, current version 0.0.0)
@rpath/libtbbmalloc.dylib (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgcc_s.1.1.dylib" "IgGeneUsage.buildbin-libdir/IgGeneUsage/libs/IgGeneUsage.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib" "IgGeneUsage.buildbin-libdir/IgGeneUsage/libs/IgGeneUsage.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib" "IgGeneUsage.buildbin-libdir/IgGeneUsage/libs/IgGeneUsage.so"
>>>>>>> Paths after fix:
IgGeneUsage.buildbin-libdir/IgGeneUsage/libs/IgGeneUsage.so:
IgGeneUsage.so (compatibility version 0.0.0, current version 0.0.0)
@rpath/libtbb.dylib (compatibility version 0.0.0, current version 0.0.0)
@rpath/libtbbmalloc.dylib (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
