Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:33:02 -0400 (Tue, 09 Apr 2019).
Package 656/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
genphen 1.11.23 Simo Kitanovski
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | [ OK ] | OK | OK | OK |
Package: genphen |
Version: 1.11.23 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL genphen |
StartedAt: 2019-04-08 18:37:46 -0400 (Mon, 08 Apr 2019) |
EndedAt: 2019-04-08 18:40:14 -0400 (Mon, 08 Apr 2019) |
EllapsedTime: 148.4 seconds |
RetCode: 0 |
Status: OK |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL genphen ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘genphen’ ... ** libs "/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/H.stan Registered S3 methods overwritten by 'ggplot2': method from [.quosures rlang c.quosures rlang print.quosures rlang Wrote C++ file "stan_files/H.cc" clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include" -I/usr/local/include -fPIC -Wall -g -O2 -c stan_files/H.cc -o stan_files/H.o In file included from stan_files/H.cc:3: In file included from stan_files/H.hpp:18: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/random/additive_combine.hpp:27: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/random/linear_congruential.hpp:30: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/random/detail/const_mod.hpp:23: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/random/detail/large_arithmetic.hpp:19: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/random/detail/integer_log2.hpp:19: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/pending/integer_log2.hpp:7:1: warning: This header is deprecated. Use <boost/integer/integer_log2.hpp> instead. [-W#pragma-messages] BOOST_HEADER_DEPRECATED("<boost/integer/integer_log2.hpp>"); ^ /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED' # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.") ^ /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE' # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) ^ <scratch space>:73:2: note: expanded from here message("This header is deprecated. Use " "<boost/integer/integer_log2.hpp>" " instead.") ^ In file included from stan_files/H.cc:3: In file included from stan_files/H.hpp:18: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:34: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/core/matrix_vari.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Dense:1: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Core:535: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stan_files/H.cc:3: In file included from stan_files/H.hpp:18: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:34: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/core/matrix_vari.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Dense:2: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/LU:47: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stan_files/H.cc:3: In file included from stan_files/H.hpp:18: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:34: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/core/matrix_vari.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Dense:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Cholesky:12: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Jacobi:29: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stan_files/H.cc:3: In file included from stan_files/H.hpp:18: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:34: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/core/matrix_vari.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Dense:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Cholesky:43: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stan_files/H.cc:3: In file included from stan_files/H.hpp:18: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:34: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/core/matrix_vari.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Dense:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/QR:17: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Householder:27: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stan_files/H.cc:3: In file included from stan_files/H.hpp:18: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:34: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/core/matrix_vari.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Dense:5: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/SVD:48: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stan_files/H.cc:3: In file included from stan_files/H.hpp:18: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:34: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/core/matrix_vari.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Dense:6: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Geometry:58: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stan_files/H.cc:3: In file included from stan_files/H.hpp:18: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:34: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/core/matrix_vari.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Dense:7: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Eigenvalues:58: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stan_files/H.cc:3: In file included from stan_files/H.hpp:18: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:34: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:96: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/csr_extract_u.hpp:6: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Sparse:26: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/SparseCore:66: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stan_files/H.cc:3: In file included from stan_files/H.hpp:18: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:34: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:96: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/csr_extract_u.hpp:6: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Sparse:27: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/OrderingMethods:71: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stan_files/H.cc:3: In file included from stan_files/H.hpp:18: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:34: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:96: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/csr_extract_u.hpp:6: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Sparse:29: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/SparseCholesky:43: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stan_files/H.cc:3: In file included from stan_files/H.hpp:18: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:34: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:96: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/csr_extract_u.hpp:6: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Sparse:32: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/SparseQR:35: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stan_files/H.cc:3: In file included from stan_files/H.hpp:18: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:34: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:96: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/csr_extract_u.hpp:6: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Sparse:33: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/IterativeLinearSolvers:46: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stan_files/H.cc:3: In file included from stan_files/H.hpp:18: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:34: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:44: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:14:13: warning: unused function 'set_zero_all_adjoints' [-Wunused-function] static void set_zero_all_adjoints() { ^ In file included from stan_files/H.cc:3: In file included from stan_files/H.hpp:18: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:34: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:70: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/autocorrelation.hpp:18:8: warning: function 'fft_next_good_size' is not needed and will not be emitted [-Wunneeded-internal-declaration] size_t fft_next_good_size(size_t N) { ^ 16 warnings generated. "/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/U.stan Registered S3 methods overwritten by 'ggplot2': method from [.quosures rlang c.quosures rlang print.quosures rlang Wrote C++ file "stan_files/U.cc" clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include" -I/usr/local/include -fPIC -Wall -g -O2 -c stan_files/U.cc -o stan_files/U.o In file included from stan_files/U.cc:3: In file included from stan_files/U.hpp:18: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/random/additive_combine.hpp:27: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/random/linear_congruential.hpp:30: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/random/detail/const_mod.hpp:23: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/random/detail/large_arithmetic.hpp:19: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/random/detail/integer_log2.hpp:19: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/pending/integer_log2.hpp:7:1: warning: This header is deprecated. Use <boost/integer/integer_log2.hpp> instead. [-W#pragma-messages] BOOST_HEADER_DEPRECATED("<boost/integer/integer_log2.hpp>"); ^ /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED' # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.") ^ /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE' # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x))) ^ <scratch space>:73:2: note: expanded from here message("This header is deprecated. Use " "<boost/integer/integer_log2.hpp>" " instead.") ^ In file included from stan_files/U.cc:3: In file included from stan_files/U.hpp:18: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:34: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/core/matrix_vari.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Dense:1: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Core:535: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stan_files/U.cc:3: In file included from stan_files/U.hpp:18: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:34: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/core/matrix_vari.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Dense:2: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/LU:47: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stan_files/U.cc:3: In file included from stan_files/U.hpp:18: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:34: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/core/matrix_vari.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Dense:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Cholesky:12: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Jacobi:29: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stan_files/U.cc:3: In file included from stan_files/U.hpp:18: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:34: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/core/matrix_vari.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Dense:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Cholesky:43: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stan_files/U.cc:3: In file included from stan_files/U.hpp:18: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:34: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/core/matrix_vari.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Dense:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/QR:17: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Householder:27: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stan_files/U.cc:3: In file included from stan_files/U.hpp:18: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:34: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/core/matrix_vari.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Dense:5: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/SVD:48: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stan_files/U.cc:3: In file included from stan_files/U.hpp:18: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:34: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/core/matrix_vari.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Dense:6: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Geometry:58: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stan_files/U.cc:3: In file included from stan_files/U.hpp:18: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:34: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/core/matrix_vari.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Dense:7: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Eigenvalues:58: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stan_files/U.cc:3: In file included from stan_files/U.hpp:18: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:34: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:96: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/csr_extract_u.hpp:6: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Sparse:26: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/SparseCore:66: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stan_files/U.cc:3: In file included from stan_files/U.hpp:18: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:34: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:96: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/csr_extract_u.hpp:6: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Sparse:27: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/OrderingMethods:71: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stan_files/U.cc:3: In file included from stan_files/U.hpp:18: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:34: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:96: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/csr_extract_u.hpp:6: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Sparse:29: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/SparseCholesky:43: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stan_files/U.cc:3: In file included from stan_files/U.hpp:18: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:34: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:96: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/csr_extract_u.hpp:6: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Sparse:32: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/SparseQR:35: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stan_files/U.cc:3: In file included from stan_files/U.hpp:18: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:34: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:96: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/csr_extract_u.hpp:6: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/Sparse:33: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/IterativeLinearSolvers:46: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] #pragma clang diagnostic pop ^ In file included from stan_files/U.cc:3: In file included from stan_files/U.hpp:18: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:34: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:44: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:14:13: warning: unused function 'set_zero_all_adjoints' [-Wunused-function] static void set_zero_all_adjoints() { ^ In file included from stan_files/U.cc:3: In file included from stan_files/U.hpp:18: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include/rstan/stan_fit.hpp:34: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12: In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:70: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/autocorrelation.hpp:18:8: warning: function 'fft_next_good_size' is not needed and will not be emitted [-Wunneeded-internal-declaration] size_t fft_next_good_size(size_t N) { ^ 16 warnings generated. clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include" -I/usr/local/include -fPIC -Wall -g -O2 -c init.cpp -o init.o clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o genphen.so stan_files/H.o stan_files/U.o init.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation rm stan_files/H.cc stan_files/U.cc installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/genphen/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 * DONE (genphen)