I recently ran into some difficulty compiling a model in RStudio that I think believe is due to HOME being different between R command line and RStudio.
/home/rstudio/.R/Makevars is not generated during container instantiation, however /root/.R/Makevars exists. HOME in R is /root. HOME in RStudio is /home/rstudio.
I believe that running install_stan.R using command line R, is why ~/.R/Makevars file is created in /root instead of /home/rstudio.
It can be confirmed that /.R/Makevars has not been properly generated by running in Rstudio: > readLines("/.R/Makevars") Error in file(con, "r") : cannot open the connection In addition: Warning message: In file(con, "r") :
cannot open file '/home/rstudio/.R/Makevars': No such file or directory
Symptoms: Stan model compile problems that depend upon the model being compiled (some simple models compile without error but schools.stan example here does not).
Correction: generating Makevars file in /home/rstudio allows schools.stan to compile.
Specific error message for schools.stan:
Error in compileCode(f, code, language = language, verbose = verbose) :
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:55:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__vector(2) double’} [-Wignored-attributes] 55 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~g++: fatal error: Killed signal terminated program cc1pluscompilation terminated.make: *** [/usr/local/lib/R/etc/Makeconf:181: file16f20d9e181.o] Error 1
before running Makevars script within RStudio, we are given this information about compiler setttings:
> mod <- stan_model("schools.stan", verbose=TRUE)
TRANSLATING MODEL 'schools' FROM Stan CODE TO C++ CODE NOW.
successful in parsing the Stan model 'schools'.
COMPILING THE C++ CODE FOR MODEL 'schools' NOW.
OS: x86_64, linux-gnu; rstan: 2.21.2; Rcpp: 1.0.6; inline: 0.3.17
>> setting environment variables:
PKG_LIBS = '/usr/local/lib/R/site-library/rstan/lib//libStanServices.a' -L'/usr/local/lib/R/site-library/StanHeaders/lib/' -lStanHeaders -L'/usr/local/lib/R/site-library/RcppParallel/lib/' -ltbb
PKG_CPPFLAGS = -I"/usr/local/lib/R/site-library/Rcpp/include/" -I"/usr/local/lib/R/site-library/RcppEigen/include/" -I"/usr/local/lib/R/site-library/RcppEigen/include/unsupported" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/StanHeaders/include/src/" -I"/usr/local/lib/R/site-library/StanHeaders/include/" -I"/usr/local/lib/R/site-library/RcppParallel/include/" -I"/usr/local/lib/R/site-library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1
>> Program source :
...
make cmd is
make -f '/usr/local/lib/R/etc/Makeconf' -f '/usr/local/lib/R/share/make/shlib.mk' CXX='$(CXX14) $(CXX14STD)' CXXFLAGS='$(CXX14FLAGS)' CXXPICFLAGS='$(CXX14PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX14LDFLAGS)' SHLIB_LD='$(SHLIB_CXX14LD)' SHLIB='file16f20d9e181.so' OBJECTS='file16f20d9e181.o'
make would use
**g++** -std=gnu++14 -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include/" -I"/usr/local/lib/R/site-library/RcppEigen/include/" -I"/usr/local/lib/R/site-library/RcppEigen/include/unsupported" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/StanHeaders/include/src/" -I"/usr/local/lib/R/site-library/StanHeaders/include/" -I"/usr/local/lib/R/site-library/RcppParallel/include/" -I"/usr/local/lib/R/site-library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c file16f20d9e181.cpp -o file16f20d9e181.o
if test "zfile16f20d9e181.o" != "z"; then \
echo g++ -std=gnu++14 -shared -L"/usr/local/lib/R/lib" -L/usr/local/lib -o file16f20d9e181.so file16f20d9e181.o '/usr/local/lib/R/site-library/rstan/lib//libStanServices.a' -L'/usr/local/lib/R/site-library/StanHeaders/lib/' -lStanHeaders -L'/usr/local/lib/R/site-library/RcppParallel/lib/' -ltbb -L"/usr/local/lib/R/lib" -lR; \
g++ -std=gnu++14 -shared -L"/usr/local/lib/R/lib" -L/usr/local/lib -o file16f20d9e181.so file16f20d9e181.o '/usr/local/lib/R/site-library/rstan/lib//libStanServices.a' -L'/usr/local/lib/R/site-library/StanHeaders/lib/' -lStanHeaders -L'/usr/local/lib/R/site-library/RcppParallel/lib/' -ltbb -L"/usr/local/lib/R/lib" -lR; \
fi
after adding the Makevars, it changes:
> mod <- stan_model("schools.stan", verbose=TRUE)
TRANSLATING MODEL 'schools' FROM Stan CODE TO C++ CODE NOW.
successful in parsing the Stan model 'schools'.
COMPILING THE C++ CODE FOR MODEL 'schools' NOW.
OS: x86_64, linux-gnu; rstan: 2.21.2; Rcpp: 1.0.6; inline: 0.3.17
>> setting environment variables:
PKG_LIBS = '/usr/local/lib/R/site-library/rstan/lib//libStanServices.a' -L'/usr/local/lib/R/site-library/StanHeaders/lib/' -lStanHeaders -L'/usr/local/lib/R/site-library/RcppParallel/lib/' -ltbb
PKG_CPPFLAGS = -I"/usr/local/lib/R/site-library/Rcpp/include/" -I"/usr/local/lib/R/site-library/RcppEigen/include/" -I"/usr/local/lib/R/site-library/RcppEigen/include/unsupported" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/StanHeaders/include/src/" -I"/usr/local/lib/R/site-library/StanHeaders/include/" -I"/usr/local/lib/R/site-library/RcppParallel/include/" -I"/usr/local/lib/R/site-library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1
>> Program source :
...
make cmd is
make -f '/usr/local/lib/R/etc/Makeconf' -f '/usr/local/lib/R/share/make/shlib.mk' -f '/home/rstudio/.R/Makevars' CXX='$(CXX14) $(CXX14STD)' CXXFLAGS='$(CXX14FLAGS)' CXXPICFLAGS='$(CXX14PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX14LDFLAGS)' SHLIB_LD='$(SHLIB_CXX14LD)' SHLIB='file16f67e794ea.so' OBJECTS='file16f67e794ea.o'
make would use
**clang++** -std=gnu++14 -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include/" -I"/usr/local/lib/R/site-library/RcppEigen/include/" -I"/usr/local/lib/R/site-library/RcppEigen/include/unsupported" -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/StanHeaders/include/src/" -I"/usr/local/lib/R/site-library/StanHeaders/include/" -I"/usr/local/lib/R/site-library/RcppParallel/include/" -I"/usr/local/lib/R/site-library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fpic -O3 -march=native -mtune=native -fPIC -c file16f67e794ea.cpp -o file16f67e794ea.o
if test "zfile16f67e794ea.o" != "z"; then \
echo clang++ -std=gnu++14 -shared -L"/usr/local/lib/R/lib" -L/usr/local/lib -o file16f67e794ea.so file16f67e794ea.o '/usr/local/lib/R/site-library/rstan/lib//libStanServices.a' -L'/usr/local/lib/R/site-library/StanHeaders/lib/' -lStanHeaders -L'/usr/local/lib/R/site-library/RcppParallel/lib/' -ltbb -L"/usr/local/lib/R/lib" -lR; \
clang++ -std=gnu++14 -shared -L"/usr/local/lib/R/lib" -L/usr/local/lib -o file16f67e794ea.so file16f67e794ea.o '/usr/local/lib/R/site-library/rstan/lib//libStanServices.a' -L'/usr/local/lib/R/site-library/StanHeaders/lib/' -lStanHeaders -L'/usr/local/lib/R/site-library/RcppParallel/lib/' -ltbb -L"/usr/local/lib/R/lib" -lR; \
fi
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