CFLAGS from R_MAKEVARS_USER no longer respected when compiling stan model

Summary:

It should be possible to set a custom Makevars file using the environment variable R_MAKEVARS_USER. This worked up until 2.18.1 (GitRev 398abb20baf6) , however it seems to be broken in 2.18.2

Description:

I use the R_MAKEVARS_USER file to set custom CFLAGS when compiling my stan models. In particular, I like to use -O0 when I am debugging the nuts and bolts of my model, and then use -O2 when I am actually running my model. In both cases, I leave out the '-g' flag since the debugging symbols slow down compiling, and are not particularly useful to me.

Reproducible Steps:

If I create a Makevar file:

CFLAGS =              -O0 -pipe  -std=gnu99 
CXXFLAGS =            -O0 -pipe -Wno-unused -std=c++11

CXX=g++

And set the appropriate environment variable, then look at the process as it is compiling, I see that my CFLAGS are ignored:

$ps aux|grep cc1
aaronjg  22382  0.0  1.0 135924 85424 pts/9    R+   22:31   0:00 /usr/lib/gcc/x86_64-linux-gnu/5/cc1plus -quiet -I /usr/share/R/include -I /home/aaronjg/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include/ -I /home/aaronjg/R/x86_64-pc-linux-gnu-library/3.5/RcppEigen/include/ -I /home/aaronjg/R/x86_64-pc-linux-gnu-library/3.5/RcppEigen/include/unsupported -I /home/aaronjg/R/x86_64-pc-linux-gnu-library/3.5/BH/include -I /home/aaronjg/R/x86_64-pc-linux-gnu-library/3.5/StanHeaders/include/src/ -I /home/aaronjg/R/x86_64-pc-linux-gnu-library/3.5/StanHeaders/include/ -I /home/aaronjg/R/x86_64-pc-linux-gnu-library/3.5/rstan/include -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D NDEBUG -D EIGEN_NO_DEBUG -D BOOST_DISABLE_ASSERTS -D _FORTIFY_SOURCE=2 file573053c287bf.cpp -quiet -dumpbase file573053c287bf.cpp -mtune=generic -march=x86-64 -auxbase-strip file573053c287bf.o -g -g -O2 -Wformat=1 -Werror=format-security -Wdate-time -std=gnu++14 -fpic -fstack-protector-strong -fstack-protector-strong -Wformat -Wformat-security -o /tmp/ccJvwHtD.s

This had worked fine in rstan 2.18.1 GitRev 398abb20baf6 (I have not yet tested it in the 2.18.1 final release)

If I set them as PKG_CFLAGS,

CFLAGS =              -O0 -pipe  -std=gnu99 
CXXFLAGS =            -O0 -pipe -Wno-unused -std=c++11

CXX=g++

PKG_CFLAGS =              -O0 -pipe  -std=gnu99 
PKG_CXXFLAGS =            -O0 -pipe -Wno-unused -std=c++11

they are included, but overridden by other CFLAGS that are coming from somewhere else.

aaronjg  22222  162  2.8 335968 227412 pts/9   R+   22:30   0:01 /usr/lib/gcc/x86_64-linux- gnu/5/cc1plus -quiet -I /usr/share/R/include -I /home/aaronjg/R/x86_64-pc-linux-gnu-library /3.5/Rcpp/include/ -I /home/aaronjg/R/x86_64-pc-linux-gnu-library/3.5/RcppEigen/include/ -I /home/aaronjg/R/x86_64-pc-linux-gnu-library/3.5/RcppEigen/include/unsupported -I /home/aaronjg/R/x86_64-pc-linux-gnu-library/3.5/BH/include -I /home/aaronjg/R/x86_64-pc-linux-gnu-library/3.5/StanHeaders/include/src/ -I /home/aaronjg/R/x86_64-pc-linux-gnu-library/3.5/StanHeaders/include/ -I /home/aaronjg/R/x86_64-pc-linux-gnu-library/3.5/rstan/include -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D NDEBUG -D EIGEN_NO_DEBUG -D BOOST_DISABLE_ASSERTS -D _FORTIFY_SOURCE=2 file567c1917208.cpp -quiet -dumpbase file567c1917208.cpp -mtune=generic -march=x86-64 -auxbase-strip file567c1917208.o -g -g -O0 -O2 -Wno-unused -Wformat=1 -Werror=format-security -Wdate-time -std=gnu++14 -std=c++11 -fpic -fstack-protector-strong -fstack-protector-strong -Wformat -Wformat-security -o -

RStan Version:

2.18.2

R Version:

R version 3.5.3 (2019-03-11)

Operating System:

Ubuntu 16.04

Start by reproducing the RStan 2.18.2 compilation with R_MAKEVARS_USER set to the shown Makevars contents, and compare the compiler command with the 2.18.1 behavior described in the issue. Trace how CFLAGS, CXXFLAGS, PKG_CFLAGS, and PKG_CXXFLAGS enter Stan model compilation; done means custom flags from R_MAKEVARS_USER are respected without unintended overrides.