Makevars location is incorrect for RStudio

[KariOlson-KD]

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