library(rstan)
stan_nb <- rstan::stan_model("mything.stan")
I'm running the above and on the second line it fails, throwing the (below) error message and a pop up saying to install xcode developer tools.
I DID install xcode developer tools (i've done this multiple times). I installed R version 3.6.3 and RStudio-1.4.1106.dmg. I have xquarts and running Mac OS X Big Sur 11.2.3 and have the gfortran compiler also installed.
Any ideas on how to fix this? not sure what to do at this point. There's a lot of information online and it would be helpful if someone has had this problem recently and knows of a solution.
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> library(rstan)
Loading required package: StanHeaders
Loading required package: ggplot2
rstan (Version 2.21.1, GitRev: 2e1f913d3ca3)
For execution on a local, multicore CPU with excess RAM we recommend calling
options(mc.cores = parallel::detectCores()).
To avoid recompilation of unchanged Stan programs, we recommend calling
rstan_options(auto_write = TRUE)
> options(mc.cores = parallel::detectCores())
> library(rstan)
> stan_nb <- rstan::stan_model("mything.stan")
sh: clang++ -mmacosx-version-min=10.13: command not found
The NEXT version of Stan will not be able to pre-process your Stan program.
Please open an issue at
https://github.com/stan-dev/stanc3/issues
if you can share or at least describe your Stan program. This will help ensure that Stan
continues to work on your Stan programs in the future. Thank you!
This message can be avoided by wrapping your function call inside suppressMessages().
make cmd is
make -f '/Library/Frameworks/R.framework/Resources/etc/Makeconf' -f '/Library/Frameworks/R.framework/Resources/share/make/shlib.mk' -f '/Users/bb/.R/Makevars' CXX='$(CXX14) $(CXX14STD)' CXXFLAGS='$(CXX14FLAGS)' CXXPICFLAGS='$(CXX14PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX14LDFLAGS)' SHLIB_LD='$(SHLIB_CXX14LD)' SHLIB='file4f038d74992.so' OBJECTS='file4f038d74992.o'
make would use
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.0/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.0/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include/" -I"/Library/Frameworks/R.framework/Versions/4.0/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c file4f038d74992.cpp -o file4f038d74992.o
if test "zfile4f038d74992.o" != "z"; then \
echo clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -Wl,-rpath,/Library/Frameworks/R.framework/Resources/lib /Library/Frameworks/R.framework/Resources/lib/libc++abi.1.dylib -L"/Library/Frameworks/R.framework/Resources/lib" -L/usr/local/lib -o file4f038d74992.so file4f038d74992.o /Library/Frameworks/R.framework/Versions/4.0/Resources/library/rstan/lib//libStanServices.a -L'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/StanHeaders/lib/' -lStanHeaders -L'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/lib/' -ltbb -ltbbmalloc -ltbbmalloc_proxy -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation; \
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -Wl,-rpath,/Library/Frameworks/R.framework/Resources/lib /Library/Frameworks/R.framework/Resources/lib/libc++abi.1.dylib -L"/Library/Frameworks/R.framework/Resources/lib" -L/usr/local/lib -o file4f038d74992.so file4f038d74992.o /Library/Frameworks/R.framework/Versions/4.0/Resources/library/rstan/lib//libStanServices.a -L'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/StanHeaders/lib/' -lStanHeaders -L'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/lib/' -ltbb -ltbbmalloc -ltbbmalloc_proxy -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation; \
fi
Error in compileCode(f, code, language = language, verbose = verbose) :
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/math/special_functions/math_fwd.hpp:879:9: note: 'isfinite' declared here bool isfinite BOOST_NO_MACRO_EXPAND(T z); ^fatal error: too many errors emitted, stopping now [-ferror-limit=]15 warnings and 20 errors generated.make: *** [file4f038d74992.o] Error 1
In addition: Warning messages:
1: In system2(CXX, args = ARGS) : error in running command
2: In file.remove(c(unprocessed, processed)) :
cannot remove file '/var/folders/cj/4rp2qqj549vc48lqqvkzsjtr0000gn/T//RtmpN0DoWO/file4f062d5a916.stan', reason 'No such file or directory'
Error in sink(type = "output") : invalid connection
>
