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Published 20 hours ago • verified publisher icon stan-dev

Compilation of 'rstanarm' survival extension failed

Open CWilhelm-Benartzi opened this issue 1 year ago • 7 comments

Using the code:

install.packages("rstanarm", repos = c("https://mc-stan.org/r-packages/", getOption("repos"))) devtools::install_github("stan-dev/rstanarm", ref = "feature/survival", build_vignettes = FALSE)

I am trying to install the survival extension of the rstanarm packages into my R version 4.2 on a Windows 10 computer. It runs until: C:/Users/wilhch00/AppData/Local/R/win-library/4.2/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:55:30: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] "C:/PROGRA~1/R/R-42~1.3/bin/x64/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/surv.stan

and then the error states that: Error in rstan::stanc(file, allow_undefined = TRUE, obfuscate_model_name = FALSE) : 0 Semantic error in 'string', line 404, column 2 to line 411, column 3:

402: } 403:
404: vector quadrature_log_cdf(vector qwts, vector log_hazard, int qnodes, int N) { ^ 405: int M = rows(log_hazard); 406: vector[M] hazard = exp(log_hazard);

Real return type required for probability functions ending in _log, _lpdf, _lupdf, _lpmf, _lupmf, _cdf, _lcdf, or _lccdf. Calls: make_cc -> <Anonymous> Execution halted make: *** [Makevars.win:28: stan_files/surv.cc] Error 1 rm stan_files/polr.cc stan_files/mvmer.cc stan_files/count.cc stan_files/lm.cc stan_files/jm.cc stan_files/bernoulli.cc stan_files/binomial.cc stan_files/continuous.cc ERROR: compilation failed for package 'rstanarm'

  • removing 'C:/Users/wilhch00/AppData/Local/R/win-library/4.2/rstanarm'
  • restoring previous 'C:/Users/wilhch00/AppData/Local/R/win-library/4.2/rstanarm' Warning messages: 1: In utils::untar(tarfile, ...) : ‘tar.exe -xf "C:\Users\wilhch00\AppData\Local\Temp\RtmpcphJws\file12c849956fc.tar.gz" -C "C:/Users/wilhch00/AppData/Local/Temp/RtmpcphJws/remotes12c83388f58"’ returned error code 1 2: In i.p(...) : installation of package ‘C:/Users/wilhch00/AppData/Local/Temp/RtmpcphJws/file12c83b9a3c1e/rstanarm_2.26.1.tar.gz’ had non-zero exit status

I have tried to also download the survival extension and building the package from R studio as well. But the same issue reoccurs. Any help would be greatly appreciated. Charlotte

CWilhelm-Benartzi avatar Feb 05 '24 12:02 CWilhelm-Benartzi

It also fails when trying to install in R 4.3.2 on Mac OS 12.7.3. Both RStan and rstanarm installed successfully, so I know the c++ toolchain works. The errors I get along the lines of this (they go on and on and on and on....)

devtools::install_github("stan-dev/rstanarm",ref = "feature/survival", build_vignettes = FALSE) Downloading GitHub repo stan-dev/rstanarm@feature/survival ── R CMD build ────────────────────────────────────────────────────────────────────────────────────────────────────── ✔ checking for file ‘/private/var/folders/q2/7rb5j6ss1xn2lg75w0yhm5ymw8z1cp/T/RtmpHZ9s6b/remoteseebe5ec79ebe/stan-dev-rstanarm-590ba0a/DESCRIPTION’ ... ─ preparing ‘rstanarm’: ✔ checking DESCRIPTION meta-information ─ cleaning src ─ running ‘cleanup’ (581ms) ─ checking for LF line-endings in source and make files and shell scripts (5.3s) ─ checking for empty or unneeded directories ─ creating default NAMESPACE file ─ building ‘rstanarm_2.32.1.tar.gz’ Warning: invalid uid value replaced by that for user 'nobody' Warning: invalid gid value replaced by that for user 'nobody'

  • installing source package ‘rstanarm’ ... ** using staged installation ** libs

using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++17 using SDK: ‘’ "/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/bernoulli.stan

Wrote C++ file "stan_files/bernoulli.cc"

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 -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/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/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/opt/R/arm64/include -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -falign-functions=64 -Wall -g -O2 -c stan_files/bernoulli.cc -o stan_files/bernoulli.o

In file included from stan_files/bernoulli.cc:3: In file included from stan_files/bernoulli.hpp:18: 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/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 stan_files/bernoulli.cc:3: In file included from stan_files/bernoulli.hpp:18: 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/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 stan_files/bernoulli.cc:3: In file included from stan_files/bernoulli.hpp:18: 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/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 stan_files/bernoulli.cc:3: In file included from stan_files/bernoulli.hpp:18: 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/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 stan_files/bernoulli.cc:3: In file included from stan_files/bernoulli.hpp:18: 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/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 stan_files/bernoulli.cc:3: In file included from stan_files/bernoulli.hpp:18: 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/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 stan_files/bernoulli.cc:3: In file included from stan_files/bernoulli.hpp:18: 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/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 stan_files/bernoulli.cc:3: In file included from stan_files/bernoulli.hpp:18: 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/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 stan_files/bernoulli.cc:3: In file included from stan_files/bernoulli.hpp:18: 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/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 stan_files/bernoulli.cc:3: In file included from stan_files/bernoulli.hpp:18: 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/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 stan_files/bernoulli.cc:3: In file included from stan_files/bernoulli.hpp:18: 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/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 stan_files/bernoulli.cc:3: In file included from stan_files/bernoulli.hpp:18: 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/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 stan_files/bernoulli.cc:3: In file included from stan_files/bernoulli.hpp:18: 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/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 stan_files/bernoulli.cc:3: In file included from stan_files/bernoulli.hpp:18: 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/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 stan_files/bernoulli.cc:3: In file included from stan_files/bernoulli.hpp:18: 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:21: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/io/r_ostream.hpp:47:31: warning: 'rstan::io::r_cout_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] virtual std::streamsize xsputn(const char_type* s, const int n) { ^ /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/streambuf:291:24: note: hidden overloaded virtual function 'std::basic_streambuf::xsputn' declared here: type mismatch at 2nd parameter ('std::streamsize' (aka 'long') vs 'const int') virtual streamsize xsputn(const char_type* __s, streamsize __n); ^ In file included from stan_files/bernoulli.cc:3: In file included from stan_files/bernoulli.hpp:18: 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:21: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/io/r_ostream.hpp:70:31: warning: 'rstan::io::r_cerr_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] virtual std::streamsize xsputn(const char_type* s, const int n) { ^ /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/streambuf:291:24: note: hidden overloaded virtual function 'std::basic_streambuf::xsputn' declared here: type mismatch at 2nd parameter ('std::streamsize' (aka 'long') vs 'const int') virtual streamsize xsputn(const char_type* __s, streamsize __n); ^ In file included from stan_files/bernoulli.cc:3: In file included from stan_files/bernoulli.hpp:18: 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:31: 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/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 stan_files/bernoulli.cc:3: In file included from stan_files/bernoulli.hpp:18: 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:31: 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:36: 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 stan_files/bernoulli.cc:3: In file included from stan_files/bernoulli.hpp:18: 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:31: 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:37: 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 stan_files/bernoulli.cc:3: In file included from stan_files/bernoulli.hpp:18: 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/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/unsupported/Eigen/../../Eigen/Core:367: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Meta.h:320:25: warning: 'result_of<Eigen::internal::scalar_cmp_op<double, double, Eigen::internal::cmp_LE> (const double &, const double &)>' is deprecated [-Wdeprecated-declarations] typedef typename std::result_of<T>::type type1; ^ /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:33:20: note: in instantiation of template class 'Eigen::internal::result_of<Eigen::internal::scalar_cmp_op<double, double, Eigen::internal::cmp_LE> (const double &, const double &)>' requested here typedef typename result_of< ^ /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:497:56: note: in instantiation of template class 'Eigen::internal::traits<Eigen::CwiseBinaryOp<Eigen::internal::scalar_cmp_op<double, double, Eigen::internal::cmp_LE>, const Eigen::ArrayWrapper<Eigen::Diagonal<const Eigen::Matrix<double, -1, -1, 0>, 0>>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op, Eigen::Array<double, -1, 1, 0>>>>' requested here template<typename Derived, typename XprKind = typename traits<Derived>::XprKind, typename StorageKind = typename traits<Derived>::StorageKind> ^ /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:149:22: note: in instantiation of default argument for 'generic_xpr_base<Eigen::CwiseBinaryOp<Eigen::internal::scalar_cmp_op<double, double, Eigen::internal::cmp_LE>, const Eigen::ArrayWrapper<Eigen::Diagonal<const Eigen::Matrix<double, -1, -1, 0>, 0>>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op, Eigen::Array<double, -1, 1, 0>>>>' required here : public internal::generic_xpr_base<CwiseBinaryOp<BinaryOp, Lhs, Rhs> >::type ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:78:10: note: in instantiation of template class 'Eigen::CwiseBinaryOpImpl<Eigen::internal::scalar_cmp_op<double, double, Eigen::internal::cmp_LE>, const Eigen::ArrayWrapper<Eigen::Diagonal<const Eigen::Matrix<double, -1, -1, 0>, 0>>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op, Eigen::Array<double, -1, 1, 0>>, Eigen::Dense>' requested here public CwiseBinaryOpImpl< ^ /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/err/check_pos_definite.hpp:47:38: note: in instantiation of template class 'Eigen::CwiseBinaryOp<Eigen::internal::scalar_cmp_op<double, double, Eigen::internal::cmp_LE>, const Eigen::ArrayWrapper<Eigen::Diagonal<const Eigen::Matrix<double, -1, -1, 0>, 0>>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op, Eigen::Array<double, -1, 1, 0>>>' requested here || (cholesky.vectorD().array() <= 0.0).any()) { ^ /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/type_traits:4009:34: note: 'result_of<Eigen::internal::scalar_cmp_op<double, double, Eigen::internal::cmp_LE> (const double &, const double &)>' has been explicitly marked deprecated here template <class _Callable> class _LIBCPP_DEPRECATED_IN_CXX17 result_of; ^ /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1066:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'

define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED

                                  ^

/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: note: expanded from macro '_LIBCPP_DEPRECATED'

define _LIBCPP_DEPRECATED attribute ((deprecated))

                                           ^

In file included from stan_files/bernoulli.cc:3: In file included from stan_files/bernoulli.hpp:18: 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/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/unsupported/Eigen/../../Eigen/Core:367: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Meta.h:320:25: warning: 'result_of<Eigen::internal::scalar_cmp_op<double, double, Eigen::internal::cmp_LT> (const double &, const double &)>' is deprecated [-Wdeprecated-declarations] typedef typename std::result_of<T>::type type1; ^ /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:33:20: note: in instantiation of template class 'Eigen::internal::result_of<Eigen::internal::scalar_cmp_op<double, double, Eigen::internal::cmp_LT> (const double &, const double &)>' requested here typedef typename result_of< ^ /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:497:56: note: in instantiation of template class 'Eigen::internal::traits<Eigen::CwiseBinaryOp<Eigen::internal::scalar_cmp_op<double, double, Eigen::internal::cmp_LT>, const Eigen::ArrayWrapper<Eigen::Diagonal<const Eigen::Matrix<double, -1, -1, 0>, 0>>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op, Eigen::Array<double, -1, 1, 0>>>>' requested here template<typename Derived, typename XprKind = typename traits<Derived>::XprKind, typename StorageKind = typename traits<Derived>::StorageKind> ^ /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:149:22: note: in instantiation of default argument for 'generic_xpr_base<Eigen::CwiseBinaryOp<Eigen::internal::scalar_cmp_op<double, double, Eigen::internal::cmp_LT>, const Eigen::ArrayWrapper<Eigen::Diagonal<const Eigen::Matrix<double, -1, -1, 0>, 0>>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op, Eigen::Array<double, -1, 1, 0>>>>' required here : public internal::generic_xpr_base<CwiseBinaryOp<BinaryOp, Lhs, Rhs> >::type ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:78:10: note: in instantiation of template class 'Eigen::CwiseBinaryOpImpl<Eigen::internal::scalar_cmp_op<double, double, Eigen::internal::cmp_LT>, const Eigen::ArrayWrapper<Eigen::Diagonal<const Eigen::Matrix<double, -1, -1, 0>, 0>>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op, Eigen::Array<double, -1, 1, 0>>, Eigen::Dense>' requested here public CwiseBinaryOpImpl< ^ /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/err/check_pos_semidefinite.hpp:46:38: note: in instantiation of template class 'Eigen::CwiseBinaryOp<Eigen::internal::scalar_cmp_op<double, double, Eigen::internal::cmp_LT>, const Eigen::ArrayWrapper<Eigen::Diagonal<const Eigen::Matrix<double, -1, -1, 0>, 0>>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op, Eigen::Array<double, -1, 1, 0>>>' requested here || (cholesky.vectorD().array() < 0.0).any()) { ^ /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/type_traits:4009:34: note: 'result_of<Eigen::internal::scalar_cmp_op<double, double, Eigen::internal::cmp_LT> (const double &, const double &)>' has been explicitly marked deprecated here template <class _Callable> class _LIBCPP_DEPRECATED_IN_CXX17 result_of; ^ /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1066:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'

define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED

                                  ^

/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: note: expanded from macro '_LIBCPP_DEPRECATED'

define _LIBCPP_DEPRECATED attribute ((deprecated))

                                           ^

In file included from stan_files/bernoulli.cc:3: In file included from stan_files/bernoulli.hpp:18: 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:43: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:35: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:57:1: warning: 'ops_partials_edge' defined as a struct template here but previously declared as a class template; this is valid, but may result in linker errors under the Microsoft C++ ABI [-Wmismatched-tags] struct ops_partials_edge<ViewElt, Op, require_st_arithmetic<Op>> { ^ /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:45:1: note: did you mean struct here? class ops_partials_edge; ^~~~~ struct In file included from stan_files/bernoulli.cc:3: In file included from stan_files/bernoulli.hpp:18: 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/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/unsupported/Eigen/../../Eigen/Core:367: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Meta.h:320:25: warning: 'result_of<Eigen::internal::scalar_product_op (const int &, const int &)>' is deprecated [-Wdeprecated-declarations] typedef typename std::result_of<T>::type type1; ^ /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:33:20: note: in instantiation of template class 'Eigen::internal::result_of<Eigen::internal::scalar_product_op (const int &, const int &)>' requested here typedef typename result_of< ^ /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:497:56: note: in instantiation of template class 'Eigen::internal::traits<Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op, const Eigen::Array<int, -1, 1, 0>>, const Eigen::ArrayWrapper<Eigen::Matrix<int, -1, 1, 0>>>>' requested here template<typename Derived, typename XprKind = typename traits<Derived>::XprKind, typename StorageKind = typename traits<Derived>::StorageKind> ^ /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:149:22: note: in instantiation of default argument for 'generic_xpr_base<Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op, const Eigen::Array<int, -1, 1, 0>>, const Eigen::ArrayWrapper<Eigen::Matrix<int, -1, 1, 0>>>>' required here : public internal::generic_xpr_base<CwiseBinaryOp<BinaryOp, Lhs, Rhs> >::type ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:78:10: note: in instantiation of template class 'Eigen::CwiseBinaryOpImpl<Eigen::internal::scalar_product_op, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op, const Eigen::Array<int, -1, 1, 0>>, const Eigen::ArrayWrapper<Eigen::Matrix<int, -1, 1, 0>>, Eigen::Dense>' requested here public CwiseBinaryOpImpl< ^ /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/grad_pFq.hpp:207:38: note: in instantiation of template class 'Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op, const Eigen::Array<int, -1, 1, 0>>, const Eigen::ArrayWrapper<Eigen::Matrix<int, -1, 1, 0>>>' requested here curr_signs_da = (base_sign * log_phammer_an_sign.array() ^ /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/type_traits:4009:34: note: 'result_of<Eigen::internal::scalar_product_op (const int &, const int &)>' has been explicitly marked deprecated here template <class _Callable> class _LIBCPP_DEPRECATED_IN_CXX17 result_of; ^ /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1066:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'

define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED

                                  ^

/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: note: expanded from macro '_LIBCPP_DEPRECATED'

define _LIBCPP_DEPRECATED attribute ((deprecated))

                                           ^

In file included from stan_files/bernoulli.cc:3: In file included from stan_files/bernoulli.hpp:18: 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/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/unsupported/Eigen/../../Eigen/Core:367: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Meta.h:320:25: warning: 'result_of<Eigen::internal::scalar_difference_op<int, double> (const int &, const double &)>' is deprecated [-Wdeprecated-declarations] typedef typename std::result_of<T>::type type1; ^ /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:33:20: note: in instantiation of template class 'Eigen::internal::result_of<Eigen::internal::scalar_difference_op<int, double> (const int &, const double &)>' requested here typedef typename result_of< ^ /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:497:56: note: in instantiation of template class 'Eigen::internal::traits<Eigen::CwiseBinaryOp<Eigen::internal::scalar_difference_op<int, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op, const Eigen::Array<int, -1, 1, 0>>, const Eigen::CwiseNullaryOp<Eigen::internal::linspaced_op<double, attribute((neon_vector_type(2))) double>, Eigen::Array<double, -1, 1, 0>>>>' requested here template<typename Derived, typename XprKind = typename traits<Derived>::XprKind, typename StorageKind = typename traits<Derived>::StorageKind> ^ /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:149:22: note: in instantiation of default argument for 'generic_xpr_base<Eigen::CwiseBinaryOp<Eigen::internal::scalar_difference_op<int, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op, const Eigen::Array<int, -1, 1, 0>>, const Eigen::CwiseNullaryOp<Eigen::internal::linspaced_op<double, attribute((neon_vector_type(2))) double>, Eigen::Array<double, -1, 1, 0>>>>' required here : public internal::generic_xpr_base<CwiseBinaryOp<BinaryOp, Lhs, Rhs> >::type ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:78:10: note: in instantiation of template class 'Eigen::CwiseBinaryOpImpl<Eigen::internal::scalar_difference_op<int, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op, const Eigen::Array<int, -1, 1, 0>>, const Eigen::CwiseNullaryOp<Eigen::internal::linspaced_op<double, attribute((neon_vector_type(2))) double>, Eigen::Array<double, -1, 1, 0>>, Eigen::Dense>' requested here public CwiseBinaryOpImpl< ^ /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/lmgamma.hpp:58:37: note: in instantiation of template class 'Eigen::CwiseBinaryOp<Eigen::internal::scalar_difference_op<int, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op, const Eigen::Array<int, -1, 1, 0>>, const Eigen::CwiseNullaryOp<Eigen::internal::linspaced_op<double, attribute((neon_vector_type(2))) double>, Eigen::Array<double, -1, 1, 0>>>' requested here return result + sum(lgamma(x + (1 - Eigen::ArrayXd::LinSpaced(k, 1, k)) / 2)); ^ /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/type_traits:4009:34: note: 'result_of<Eigen::internal::scalar_difference_op<int, double> (const int &, const double &)>' has been explicitly marked deprecated here template <class _Callable> class _LIBCPP_DEPRECATED_IN_CXX17 result_of; ^ /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1066:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'

define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED

                                  ^

/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: note: expanded from macro '_LIBCPP_DEPRECATED'

define _LIBCPP_DEPRECATED attribute ((deprecated))

                                           ^

In file included from stan_files/bernoulli.cc:3: In file included from stan_files/bernoulli.hpp:18: 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/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/unsupported/Eigen/../../Eigen/Core:367: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Meta.h:320:25: warning: 'result_of<Eigen::internal::scalar_quotient_op<double, int> (const double &, const int &)>' is deprecated [-Wdeprecated-declarations] typedef typename std::result_of<T>::type type1; ^ /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:33:20: note: in instantiation of template class 'Eigen::internal::result_of<Eigen::internal::scalar_quotient_op<double, int> (const double &, const int &)>' requested here typedef typename result_of< ^ /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:497:56: note: in instantiation of template class 'Eigen::internal::traits<Eigen::CwiseBinaryOp<Eigen::internal::scalar_quotient_op<double, int>, const Eigen::CwiseBinaryOp<Eigen::internal::scalar_difference_op<int, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op, const Eigen::Array<int, -1, 1, 0>>, const Eigen::CwiseNullaryOp<Eigen::internal::linspaced_op<double, attribute((neon_vector_type(2))) double>, Eigen::Array<double, -1, 1, 0>>>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op, const Eigen::Array<int, -1, 1, 0>>>>' requested here template<typename Derived, typename XprKind = typename traits<Derived>::XprKind, typename StorageKind = typename traits<Derived>::StorageKind> ^ /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:149:22: note: in instantiation of default argument for 'generic_xpr_base<Eigen::CwiseBinaryOp<Eigen::internal::scalar_quotient_op<double, int>, const Eigen::CwiseBinaryOp<Eigen::internal::scalar_difference_op<int, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op, const Eigen::Array<int, -1, 1, 0>>, const Eigen::CwiseNullaryOp<Eigen::internal::linspaced_op<double, attribute((neon_vector_type(2))) double>, Eigen::Array<double, -1, 1, 0>>>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op, const Eigen::Array<int, -1, 1, 0>>>>' required here : public internal::generic_xpr_base<CwiseBinaryOp<BinaryOp, Lhs, Rhs> >::type ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:78:10: note: in instantiation of template class 'Eigen::CwiseBinaryOpImpl<Eigen::internal::scalar_quotient_op<double, int>, const Eigen::CwiseBinaryOp<Eigen::internal::scalar_difference_op<int, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op, const Eigen::Array<int, -1, 1, 0>>, const Eigen::CwiseNullaryOp<Eigen::internal::linspaced_op<double, attribute((neon_vector_type(2))) double>, Eigen::Array<double, -1, 1, 0>>>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op, const Eigen::Array<int, -1, 1, 0>>, Eigen::Dense>' requested here public CwiseBinaryOpImpl< ^ /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/lmgamma.hpp:58:75: note: in instantiation of template class 'Eigen::CwiseBinaryOp<Eigen::internal::scalar_quotient_op<double, int>, const Eigen::CwiseBinaryOp<Eigen::internal::scalar_difference_op<int, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op, const Eigen::Array<int, -1, 1, 0>>, const Eigen::CwiseNullaryOp<Eigen::internal::linspaced_op<double, attribute((neon_vector_type(2))) double>, Eigen::Array<double, -1, 1, 0>>>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op, const Eigen::Array<int, -1, 1, 0>>>' requested here return result + sum(lgamma(x + (1 - Eigen::ArrayXd::LinSpaced(k, 1, k)) / 2)); ^ /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/type_traits:4009:34: note: 'result_of<Eigen::internal::scalar_quotient_op<double, int> (const double &, const int &)>' has been explicitly marked deprecated here template <class _Callable> class _LIBCPP_DEPRECATED_IN_CXX17 result_of; ^ /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1066:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'

define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED

                                  ^

/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: note: expanded from macro '_LIBCPP_DEPRECATED'

define _LIBCPP_DEPRECATED attribute ((deprecated))

                                           ^

In file included from stan_files/bernoulli.cc:3: In file included from stan_files/bernoulli.hpp:18: 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/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/unsupported/Eigen/../../Eigen/Core:367: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Meta.h:320:25: warning: 'result_of<Eigen::internal::scalar_product_op (const double &, const double &)>' is deprecated [-Wdeprecated-declarations] typedef typename std::result_of<T>::type type1; ^ /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:33:20: note: in instantiation of template class 'Eigen::internal::result_of<Eigen::internal::scalar_product_op (const double &, const double &)>' requested here typedef typename result_of< ^ /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:497:56: note: in instantiation of template class 'Eigen::internal::traits<Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op, const Eigen::Matrix<double, -1, -1, 0>>, const Eigen::Product<Eigen::Matrix<double, -1, -1, 0>, Eigen::Matrix<double, -1, -1, 0>, 0>>>' requested here template<typename Derived, typename XprKind = typename traits<Derived>::XprKind, typename StorageKind = typename traits<Derived>::StorageKind> ^ /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:149:22: note: in instantiation of default argument for 'generic_xpr_base<Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op, const Eigen::Matrix<double, -1, -1, 0>>, const Eigen::Product<Eigen::Matrix<double, -1, -1, 0>, Eigen::Matrix<double, -1, -1, 0>, 0>>>' required here : public internal::generic_xpr_base<CwiseBinaryOp<BinaryOp, Lhs, Rhs> >::type ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:78:10: note: in instantiation of template class 'Eigen::CwiseBinaryOpImpl<Eigen::internal::scalar_product_op, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op, const Eigen::Matrix<double, -1, -1, 0>>, const Eigen::Product<Eigen::Matrix<double, -1, -1, 0>, Eigen::Matrix<double, -1, -1, 0>, 0>, Eigen::Dense>' requested here public CwiseBinaryOpImpl< ^ /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/matrix_exp_action_handler.hpp:86:34: note: in instantiation of template class 'Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op, const Eigen::Matrix<double, -1, -1, 0>>, const Eigen::Product<Eigen::Matrix<double, -1, -1, 0>, Eigen::Matrix<double, -1, -1, 0>, 0>>' requested here bi = (t / (s * (j + 1))) * (A * bi); ^ /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/type_traits:4009:34: note: 'result_of<Eigen::internal::scalar_product_op (const double &, const double &)>' has been explicitly marked deprecated here template <class _Callable> class _LIBCPP_DEPRECATED_IN_CXX17 result_of; ^ /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1066:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'

define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED

                                  ^

/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: note: expanded from macro '_LIBCPP_DEPRECATED'

define _LIBCPP_DEPRECATED attribute ((deprecated))

                                           ^

In file included from stan_files/bernoulli.cc:3: In file included from stan_files/bernoulli.hpp:18: 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/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/unsupported/Eigen/../../Eigen/Core:367: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Meta.h:320:25: warning: 'result_of<Eigen::internal::scalar_abs_op (const double &)>' is deprecated [-Wdeprecated-declarations] typedef typename std::result_of<T>::type type1; ^ /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseUnaryOp.h:21:20: note: in instantiation of template class 'Eigen::internal::result_of<Eigen::internal::scalar_abs_op (const double &)>' requested here typedef typename result_of< ^ /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:497:56: note: in instantiation of template class 'Eigen::internal::traits<Eigen::CwiseUnaryOp<Eigen::internal::scalar_abs_op, const Eigen::Matrix<double, -1, -1, 0>>>' requested here template<typename Derived, typename XprKind = typename traits<Derived>::XprKind, typename StorageKind = typename traits<Derived>::StorageKind> ^ /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseUnaryOp.h:95:22: note: in instantiation of default argument for 'generic_xpr_base<Eigen::CwiseUnaryOp<Eigen::internal::scalar_abs_op, const Eigen::Matrix<double, -1, -1, 0>>>' required here : public internal::generic_xpr_base<CwiseUnaryOp<UnaryOp, XprType> >::type ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseUnaryOp.h:55:29: note: in instantiation of template class 'Eigen::CwiseUnaryOpImpl<Eigen::internal::scalar_abs_op, const Eigen::Matrix<double, -1, -1, 0>, Eigen::Dense>' requested here class CwiseUnaryOp : public CwiseUnaryOpImpl<UnaryOp, XprType, typename internal::traits<XprType>::StorageKind>, internal::no_assignment_operator ^ /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/matrix_exp_action_handler.hpp:106:14: note: in instantiation of template class 'Eigen::CwiseUnaryOp<Eigen::internal::scalar_abs_op, const Eigen::Matrix<double, -1, -1, 0>>' requested here return x.cwiseAbs().rowwise().sum().maxCoeff(); ^ /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/type_traits:4009:34: note: 'result_of<Eigen::internal::scalar_abs_op (const double &)>' has been explicitly marked deprecated here template <class _Callable> class _LIBCPP_DEPRECATED_IN_CXX17 result_of; ^ /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1066:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'

define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED

                                  ^

/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: note: expanded from macro '_LIBCPP_DEPRECATED'

define _LIBCPP_DEPRECATED attribute ((deprecated))

                                           ^

In file included from stan_files/bernoulli.cc:3: In file included from stan_files/bernoulli.hpp:18: 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/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/unsupported/Eigen/../../Eigen/Core:367: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Meta.h:320:25: warning: 'result_of<Eigen::internal::scalar_ceil_op (const double &)>' is deprecated [-Wdeprecated-declarations] typedef typename std::result_of<T>::type type1; ^ /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseUnaryOp.h:21:20: note: in instantiation of template class 'Eigen::internal::result_of<Eigen::internal::scalar_ceil_op (const double &)>' requested here typedef typename result_of< ^ /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:497:56: note: in instantiation of template class 'Eigen::internal::traits<Eigen::CwiseUnaryOp<Eigen::internal::scalar_ceil_op, const Eigen::ArrayWrapper<const Eigen::Matrix<double, -1, -1, 0>>>>' requested here template<typename Derived, typename XprKind = typename traits<Derived>::XprKind, typename StorageKind = typename traits<Derived>::StorageKind> ^ /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseUnaryOp.h:95:22: note: in instantiation of default argument for 'generic_xpr_base<Eigen::CwiseUnaryOp<Eigen::internal::scalar_ceil_op, const Eigen::ArrayWrapper<const Eigen::Matrix<double, -1, -1, 0>>>>' required here : public internal::generic_xpr_base<CwiseUnaryOp<UnaryOp, XprType> >::type ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseUnaryOp.h:55:29: note: in instantiation of template class 'Eigen::CwiseUnaryOpImpl<Eigen::internal::scalar_ceil_op, const Eigen::ArrayWrapper<const Eigen::Matrix<double, -1, -1, 0>>, Eigen::Dense>' requested here class CwiseUnaryOp : public CwiseUnaryOpImpl<UnaryOp, XprType, typename internal::traits<XprType>::StorageKind>, internal::no_assignment_operator ^ /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/ceil.hpp:57:47: note: in instantiation of template class 'Eigen::CwiseUnaryOp<Eigen::internal::scalar_ceil_op, const Eigen::ArrayWrapper<const Eigen::Matrix<double, -1, -1, 0>>>' requested here x, [](const auto& v) { return v.array().ceil(); }); ^ /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/functor/apply_vector_unary.hpp:47:24: note: in instantiation of function template specialization 'stan::math::ceil(const Eigen::Matrix<double, -1, -1, 0> &)::(anonymous class)::operator()<Eigen::Matrix<double, -1, -1, 0>>' requested here f(x)); ^ /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/ceil.hpp:56:41: note: in instantiation of function template specialization 'stan::math::apply_vector_unary<Eigen::Matrix<double, -1, -1, 0>>::apply<(lambda at /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/ceil.hpp:57:10), Eigen::Matrix<double, -1, -1, 0>, nullptr>' requested here return apply_vector_unary<Container>::apply( ^ /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/matrix_exp_action_handler.hpp:197:37: note: in instantiation of function template specialization 'stan::math::ceil<Eigen::Matrix<double, -1, -1, 0>, nullptr, nullptr>' requested here Eigen::MatrixXd c = stan::math::ceil(mt) * u.asDiagonal(); ^ /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/type_traits:4009:34: note: 'result_of<Eigen::internal::scalar_ceil_op (const double &)>' has been explicitly marked deprecated here template <class _Callable> class _LIBCPP_DEPRECATED_IN_CXX17 result_of; ^ /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1066:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'

define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED

                                  ^

/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: note: expanded from macro '_LIBCPP_DEPRECATED'

define _LIBCPP_DEPRECATED attribute ((deprecated))

                                           ^

In file included from stan_files/bernoulli.cc:3: In file included from stan_files/bernoulli.hpp:18: 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/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/unsupported/Eigen/../../Eigen/Core:367: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Meta.h:320:25: warning: 'result_of<Eigen::internal::scalar_difference_op (const double &, const double &)>' is deprecated [-Wdeprecated-declarations] typedef typename std::result_of<T>::type type1; ^ /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:33:20: note: in instantiation of template class 'Eigen::internal::result_of<Eigen::internal::scalar_difference_op (const double &, const double &)>' requested here typedef typename result_of< ^ /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:497:56: note: in instantiation of template class 'Eigen::internal::traits<Eigen::CwiseBinaryOp<Eigen::internal::scalar_difference_op, const Eigen::Matrix<double, -1, 1, 0>, const Eigen::Matrix<double, -1, 1, 0>>>' requested here template<typename Derived, typename XprKind = typename traits<Derived>::XprKind, typename StorageKind = typename traits<Derived>::StorageKind> ^ /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:149:22: note: in instantiation of default argument for 'generic_xpr_base<Eigen::CwiseBinaryOp<Eigen::internal::scalar_difference_op, const Eigen::Matrix<double, -1, 1, 0>, const Eigen::Matrix<double, -1, 1, 0>>>' required here : public internal::generic_xpr_base<CwiseBinaryOp<BinaryOp, Lhs, Rhs> >::type ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:78:10: note: in instantiation of template class 'Eigen::CwiseBinaryOpImpl<Eigen::internal::scalar_difference_op, const Eigen::Matrix<double, -1, 1, 0>, const Eigen::Matrix<double, -1, 1, 0>, Eigen::Dense>' requested here public CwiseBinaryOpImpl< ^ /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/welford_covar_estimator.hpp:26:29: note: in instantiation of template class 'Eigen::CwiseBinaryOp<Eigen::internal::scalar_difference_op, const Eigen::Matrix<double, -1, 1, 0>, const Eigen::Matrix<double, -1, 1, 0>>' requested here Eigen::VectorXd delta(q - m_); ^ /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/type_traits:4009:34: note: 'result_of<Eigen::internal::scalar_difference_op (const double &, const double &)>' has been explicitly marked deprecated here template <class _Callable> class _LIBCPP_DEPRECATED_IN_CXX17 result_of; ^ /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1066:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'

define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED

                                  ^

/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: note: expanded from macro '_LIBCPP_DEPRECATED'

define _LIBCPP_DEPRECATED attribute ((deprecated))

                                           ^

In file included from stan_files/bernoulli.cc:3: In file included from stan_files/bernoulli.hpp:18: 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/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/unsupported/Eigen/../../Eigen/Core:367: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Meta.h:320:25: warning: 'result_of<Eigen::internal::scalar_quotient_op (const double &, const double &)>' is deprecated [-Wdeprecated-declarations] typedef typename std::result_of<T>::type type1; ^ /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:33:20: note: in instantiation of template class 'Eigen::internal::result_of<Eigen::internal::scalar_quotient_op (const double &, const double &)>' requested here typedef typename result_of< ^ /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:497:56: note: in instantiation of template class 'Eigen::internal::traits<Eigen::CwiseBinaryOp<Eigen::internal::scalar_quotient_op, const Eigen::Matrix<double, -1, 1, 0>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op, const Eigen::Matrix<double, -1, 1, 0>>>>' requested here template<typename Derived, typename XprKind = typename traits<Derived>::XprKind, typename StorageKind = typename traits<Derived>::StorageKind> ^ /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:149:22: note: in instantiation of default argument for 'generic_xpr_base<Eigen::CwiseBinaryOp<Eigen::internal::scalar_quotient_op, const Eigen::Matrix<double, -1, 1, 0>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op, const Eigen::Matrix<double, -1, 1, 0>>>>' required here : public internal::generic_xpr_base<CwiseBinaryOp<BinaryOp, Lhs, Rhs> >::type ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:78:10: note: in instantiation of template class 'Eigen::CwiseBinaryOpImpl<Eigen::internal::scalar_quotient_op, const Eigen::Matrix<double, -1, 1, 0>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op, const Eigen::Matrix<double, -1, 1, 0>>, Eigen::Dense>' requested here public CwiseBinaryOpImpl< ^ /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/welford_covar_estimator.hpp:27:17: note: in instantiation of template class 'Eigen::CwiseBinaryOp<Eigen::internal::scalar_quotient_op, const Eigen::Matrix<double, -1, 1, 0>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op, const Eigen::Matrix<double, -1, 1, 0>>>' requested here m_ += delta / num_samples_; ^ /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/type_traits:4009:34: note: 'result_of<Eigen::internal::scalar_quotient_op (const double &, const double &)>' has been explicitly marked deprecated here template <class _Callable> class _LIBCPP_DEPRECATED_IN_CXX17 result_of; ^ /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1066:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'

define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED

                                  ^

/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: note: expanded from macro '_LIBCPP_DEPRECATED'

define _LIBCPP_DEPRECATED attribute ((deprecated))

                                           ^

andrewbcooper avatar Feb 12 '24 15:02 andrewbcooper

For what it's worth, downloading the zip file from the '<> Code` dropdown and the using devtools::install_local( "rstanarm-feature-survival.zip") still threw out the above warning messages, but it successfully installed.

andrewbcooper avatar Feb 12 '24 19:02 andrewbcooper

Many thanks Andrew, just to note it still did not install for me. The error I am getting is now:

**Error: package or namespace load failed for 'rstanarm' in .doLoadActions(where, attach): error in load action .A.1 for package rstanarm: is(module, "character"): object 'm' not found Error: loading failed Execution halted ERROR: loading failed

  • removing 'C:/Users/wilhch00/AppData/Local/R/win-library/4.2/rstanarm'
  • restoring previous 'C:/Users/wilhch00/AppData/Local/R/win-library/4.2/rstanarm' Warning messages: 1: In utils::untar(tarfile, ...) : ‘tar.exe -xf "C:\Users\wilhch00\AppData\Local\Temp\Rtmpw5e0zf\file51446482430.tar.gz" -C "C:/Users/wilhch00/AppData/Local/Temp/Rtmpw5e0zf/remotes51447f8f3c02"’ returned error code 1 2: In i.p(...) : installation of package ‘C:/Users/wilhch00/AppData/Local/Temp/Rtmpw5e0zf/file51447e307c6d/rstanarm_2.32.1.tar.gz’ had non-zero exit status**

Reminder that my code is:

install.packages("rstanarm", repos = c("https://mc-stan.org/r-packages/", getOption("repos"))) devtools::install_github("stan-dev/rstanarm", ref = "feature/survival", build_vignettes = FALSE)

and I am trying to install the survival extension of the rstanarm packages into my R version 4.2 on a Windows 10 computer. Many thanks for any help you can provide. Charlotte

CWilhelm-Benartzi avatar Feb 21 '24 11:02 CWilhelm-Benartzi

Hi Charlotte,

Sorry for the delay. First thing I did was download was click the code button in the upper right corner: Screen Shot 2024-02-19 at 9 43 41 AM

Then downloaded the Zip file: Screen Shot 2024-02-19 at 9 41 52 AM

And then in the RStudio console, I typed:

devtools::install_local("~/Downloads/rstanarm-feature-survival.zip")

And it worked.

andrewbcooper avatar Feb 26 '24 22:02 andrewbcooper

Thank you so much! This worked for me too! All the best, Charlotte

CWilhelm-Benartzi avatar Feb 27 '24 09:02 CWilhelm-Benartzi

Hello, I also downloaded the zip file to downloads and used the code devtools::install_local("~/Downloads/rstanarm-feature-survival.zip"), it gives me following error message

Error : Could not copy `C:\Users\hazel2544\Documents\Downloads\rstanarm-feature-survival.zip` to `C:\Users\hazel2544\AppData\Local\Temp\1\RtmpKqr3LA\fileaa018702cd3`
In addition: Warning message:
In normalizePath(path.expand(path), winslash, mustWork) :
  path[1]="Downloads/rstanarm-feature-survival.zip": The system cannot find the path specified

Could anyone please help? Thanks very much in advanced.

Hazel2544 avatar Apr 17 '24 01:04 Hazel2544

Hello, I also downloaded the zip file to downloads and used the code devtools::install_local("~/Downloads/rstanarm-feature-survival.zip"), it gives me following error message

Error : Could not copy `C:\Users\hazel2544\Documents\Downloads\rstanarm-feature-survival.zip` to `C:\Users\hazel2544\AppData\Local\Temp\1\RtmpKqr3LA\fileaa018702cd3`
In addition: Warning message:
In normalizePath(path.expand(path), winslash, mustWork) :
  path[1]="Downloads/rstanarm-feature-survival.zip": The system cannot find the path specified

Could anyone please help? Thanks very much in advanced.

Hi @Hazel2544, The code example used a relative path ~Downloads/. Since your download folder is not under your current R session working directory, you need to put the absolute path to the folder where you downloaded the zip file as follows: devtools::install_local(<path/to/zip file>) (just replace <path/to/zip file> by your actual file path)

IanOndo avatar Apr 28 '24 17:04 IanOndo