Hello,
I was having the same problem with Rstan version 2.12.2 not compiling and tried reverting to 2.19.3 with the code you sent but it gives me this error:
packageurl ← “http://cran.r-project.org/src/contrib/Archive/rstan/rstan_2.19.3.tar.gz”
install.packages(packageurl, repos = NULL, type = “source”)
trying URL ‘http://cran.r-project.org/src/contrib/Archive/rstan/rstan_2.19.3.tar.gz’
Content type ‘application/x-gzip’ length 922337 bytes (900 KB)
==================================================
downloaded 900 KB
- installing source package ‘rstan’ …
** package ‘rstan’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
clang++ -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"…/inst/include" -I"." -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -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"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c chains.cpp -o chains.o
clang: warning: no such sysroot directory: ‘/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk’ [-Wmissing-sysroot]
In file included from chains.cpp:19:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/mean.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/prim/arr/err/check_nonzero_size.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/prim/meta.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/prim/arr/meta/get.hpp:4:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/…/include/c++/v1/cstdlib:85:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/…/include/c++/v1/stdlib.h:93:15: fatal error: ‘stdlib.h’ file not found
#include_next <stdlib.h>
^~~~~~~~~~
clang++ -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"…/inst/include" -I"." -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -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"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c init.cpp -o init.o
clang: warning: no such sysroot directory: ‘/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk’ [-Wmissing-sysroot]
In file included from init.cpp:25:
In file included from /Library/Frameworks/R.framework/Resources/include/R.h:47:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/…/include/c++/v1/cstdlib:85:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/…/include/c++/v1/stdlib.h:93:15: fatal error: ‘stdlib.h’ file not found
#include_next <stdlib.h>
^~~~~~~~~~
1 error generated.
make: *** [init.o] Error 1
make: *** Waiting for unfinished jobs…
1 error generated.
make: *** [chains.o] Error 1
ERROR: compilation failed for package ‘rstan’
- removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rstan’
Warning in install.packages :
installation of package ‘/var/folders/_v/_dp_x44j2_gb3fg47_bgdrxw0000gn/T//Rtmp0q7TYZ/downloaded_packages/rstan_2.19.3.tar.gz’ had non-zero exit status
I’m using macOS Catalina version 10.15.6
brms version: 2.13.5
R version: 3.6.0
Thanks