rstan or cmdstanr packages don't work

[lsaravia]

I used the template to create a binder repository

https://github.com/lsaravia/binder-rethinking

in the Install.R file

install.packages(c("StanHeaders","rstan"),type="source")

or

install.packages("rstan", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))

in both cases the package seems to be well installed but when I test the installation using:

example(stan_model, package = "rstan", run.dontrun = TRUE)
Loading required package: StanHeaders

rstan version 2.26.13 (Stan version 2.26.1)

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)
For within-chain threading using `reduce_sum()` or `map_rect()` Stan functions,
change `threads_per_chain` option:
rstan_options(threads_per_chain = 1)
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='file273f221760.so' OBJECTS='file273f221760.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  -DUSE_STANC3 -DSTRICT_R_HEADERS  -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION  -DBOOST_NO_AUTO_PTR  -include '/usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/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 file273f221760.cpp -o file273f221760.o
if test  "zfile273f221760.o" != "z"; then \
  echo g++ -std=gnu++14 -shared -L"/usr/local/lib/R/lib" -L/usr/local/lib -o file273f221760.so file273f221760.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 file273f221760.so file273f221760.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

Here binder virtual machine hangs

A similar thing happens when I also install cmdstanr I think that could be the same problem.

[eddelbuettel]

Shooting from the hip: the combination of 'C++ involved' and 'hangs or crashes' in conjunction with a VM or container is most often related to a lack of memory. Can you try the same installation commands, and test example, in a normal machine? It may just be that the (free, if I am not mistaken) binder resources are limited in scope.

[lsaravia]

So the solution would be to create a docker image with rstan and cmdstanr already compiled.

[eddelbuettel]

Yes relying on binaries removes the constraint of small system while building.

It does not remove the constraint of a small system when running. Binder sessions, free as they are, may not be suitable for all stan applications if and when those involve C++ compilations.