bug#60200: Incompatibilities between gcc-toolchain and R packages

[Lars-Dominik Braun]

Hi,

I ran into issues with the package r-brms. Take the following reproducer as an 
example:

    $ guix shell r-brms r make sed gcc-toolchain bash -C --no-cwd --share=/tmp
        $ R
        > library(brms)
        > fit1 <- brm(count ~ zAge + zBase * Trt + (1|patient), data = 
epilepsy, family = poisson())
        Compiling Stan program...
    Error in dyn.load(libLFile) :
          unable to load shared object '/tmp/RtmpKqzbYg/file3245e787c.so':
          
/gnu/store/vqhamsanmlm8v6f90a635zc6gmhwlphp-gfortran-10.3.0-lib/lib/libstdc++.so.6:
 version `GLIBCXX_3.4.29' not found (required by 
/tmp/RtmpKqzbYg/file3245e787c.so)
        Error in sink(type = "output") : invalid connection

The same code works well with gcc-toolchain@10 instead of gcc-toolchain
(@12, which is the default). As we can see the generated shared library
above depends on GCC 12, 10 and GFortran 10 at the same time:

        $ ldd /tmp/RtmpKqzbYg/file3245e787c.so | grep -e gcc -e fortran
        libstdc++.so.6 => 
/gnu/store/4zvswpr2h3b7dvqpvjcdam8vfhyjrmgl-gcc-12.2.0-lib/lib/libstdc++.so.6 
(0x00007f69bd9fc000)
        libgcc_s.so.1 => 
/gnu/store/4zvswpr2h3b7dvqpvjcdam8vfhyjrmgl-gcc-12.2.0-lib/lib/libgcc_s.so.1 
(0x00007f69bd898000)
        libgfortran.so.5 => 
/gnu/store/vqhamsanmlm8v6f90a635zc6gmhwlphp-gfortran-10.3.0-lib/lib/libgfortran.so.5
 (0x00007f69bd3e6000)
        libquadmath.so.0 => 
/gnu/store/094bbaq6glba86h1d4cj16xhdi6fk2jl-gcc-10.3.0-lib/lib/libquadmath.so.0 
(0x00007f69bd39b000)
        libgomp.so.1 => 
/gnu/store/094bbaq6glba86h1d4cj16xhdi6fk2jl-gcc-10.3.0-lib/lib/libgomp.so.1 
(0x00007f69bccf9000)

The command used to link that .so is revealed by strace to be (filenames
are random and may differ between runs):

        ["g++", "-std=gnu++14", "-shared", 
"-L/gnu/store/145dmr8drw3yzrdhzbsksi05p599hrs6-r-minimal-4.2.2/lib/R/lib", 
"-L/usr/local/lib", "-o", "file3373276d0.so", "file3373276d0.o", 
"/gnu/store/5rdg6sv1nrg1ikqxcykvdh9g4yd2xjvy-r-rstan-2.21.7/site-library/rstan/lib//libStanServices.a",
 
"-L/gnu/store/y7rvp47mz3hcnpvnqsx42qz5yvs10pnl-r-stanheaders-2.21.0-7/site-library/StanHeaders/lib/",
 "-lStanHeaders", 
"-L/gnu/store/01lhjrrkvrnsjd8xh4ssdn3bgxc422jl-r-rcppparallel-5.1.5/site-library/RcppParallel/lib/",
 "-ltbb", 
"-L/gnu/store/145dmr8drw3yzrdhzbsksi05p599hrs6-r-minimal-4.2.2/lib/R/lib", 
"-lR"]

So it links against libStanServices.a, libStanHeaders(.a), libtbb(.so) and
libR(.so) of which only libR has a reference to gfortran:

        $ ldd 
/gnu/store/145dmr8drw3yzrdhzbsksi05p599hrs6-r-minimal-4.2.2/lib/R/lib/libR.so | 
grep -i fortran
        libgfortran.so.5 => 
/gnu/store/vqhamsanmlm8v6f90a635zc6gmhwlphp-gfortran-10.3.0-lib/lib/libgfortran.so.5
 (0x00007f5be49db000)

That means every software linking against R is also incompatible with
the current default gcc-toolchain (when using the command line or
specifications; different story when writing package recipes).

Possible solutions:

- Make gcc-toolchain@10 the default and rename gcc-toolchain@12 to
  gcc-toolchain-next@12, like we do for Haskell and (sometimes) Python.
- Update, both, the default GCC and GFortran to version 12.
- Explicitly depend on the correct gcc-toolchain in packages that need
  a compiler.

Cheers,
Lars