rstan/develop doesn't work with stan/develop

Summary:

The develop branch of rstan does not work with the develop branch of stan.

Description:

The developer process overview says that submitted changes should keep all develop branches in working order. I am trying to make a change to stan in order to incorporate it into rstan. (https://github.com/stan-dev/stan/issues/2692 and https://github.com/stan-dev/rstan/issues/587). However, it seems that two two develop branches do not work together.

Reproducible Steps:

Update the install_StanHeaders.R to check out the devlop branches.

path_rstan <- tempfile(pattern = "git2r-")
print(path_rstan)
# Here, put whatever local directory has up-to-date versions of the git repo.
path_stan_dev <- "/home/rgiordan/Documents/git_repos/stan-dev/"

 git2r::clone(file.path(path_stan_dev, "rstan"),
              path_rstan, branch = "develop")

 git2r::clone(file.path(path_stan_dev, "stan"),
              file.path(path_rstan, "StanHeaders", "inst", "include", "upstream"),
              branch = "develop")

# The master branch of math seems to be required for cvodes.
 git2r::clone(file.path(path_stan_dev, "math"),
              file.path(path_rstan, "StanHeaders", "inst", "include", "mathlib"),
              branch = "master")

devtools::install(file.path(path_rstan, "StanHeaders"), args = "--preclean")

After running the above install_StanHeaders.R script, run make clean, make build, and make install in stan-dev/rstan/rstan.

Current Output:

... lots of warnings, and the error:

g++ -std=gnu++14 -I/usr/share/R/include -DNDEBUG -I"../inst/include" -I"`"/usr/lib/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -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/BH/include" -I"/usr/local/lib/R/site-library/StanHeaders/include"    -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lang__grammars__var_deccls_grammar_inst.cpp -o lang__grammars__var_deccls_grammar_inst.o
lang__grammars__var_deccls_grammar_inst.cpp:19:57: fatal error: stan/lang/grammars/var_decls_grammar_inst.cpp: No such file or directory
compilation terminated.
/usr/lib/R/etc/Makeconf:168: recipe for target 'lang__grammars__var_deccls_grammar_inst.o' failed

Expected Output:

A successful install of rstan.

RStan Version:

N/A

R Version:

N/A

Operating System:

Ubuntu 16.04

Start with the install_StanHeaders.R reproduction, checking out the develop branches of rstan and stan and master for math. Run make clean, make build, and make install in rstan, then investigate the missing stan/lang/grammars/var_decls_grammar_inst.cpp error. Done means the rstan develop branch installs successfully with the stan develop branch.