Subject: Incompatibilities between gcc-toolchain and R packages

From: Lars-Dominik Braun <[email-masked]>
Date: Mon, 19 Dec 2022 13:00:02 +0100

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