rPackages, R: R 4.3.3 -> 4.4.1 and bump rPackages

[jbedo]

Update R and rPackages.

Hydra: https://hydra.nixos.org/jobset/nixpkgs/r-updates

nixpkgs-review:

7 packages failed to build:
cantor jasp-desktop labplot python311Packages.rpy2 python311Packages.rpy2.dist sage sageWithDoc

41 packages built:
R R.tex diffoscope diffoscope.dist diffoscope.man jetbrains.dataspell ocamlPackages.ocaml-r postgresql12JitPackages.plr postgresql12Packages.plr postgresql13JitPackages.plr postgresql13Packages.plr postgresql14JitPackages.plr postgresql14Packages.plr postgresql15JitPackages.plr postgresql15Packages.plr postgresql16JitPackages.plr postgresql16Packages.plr python311Packages.cnvkit python311Packages.cnvkit.dist python311Packages.radian python311Packages.radian.dist python311Packages.rchitect python311Packages.rchitect.dist python312Packages.cnvkit python312Packages.cnvkit.dist python312Packages.radian python312Packages.radian.dist python312Packages.rchitect python312Packages.rchitect.dist python312Packages.rpy2 python312Packages.rpy2.dist quarto rWrapper radianWrapper rstudio rstudio-server rstudioServerWrapper rstudioWrapper spark spark_3_4 vscode-extensions.reditorsupport.r

jasp-desktop has warnings being elevated to errors, e.g.,:

jaspObject.cpp:508:25: error: format not a string literal and no format arguments [8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wformat-security-Werror=format-security8;;]
  508 |                 Rf_error(("nested key \"" + nestedKeyToString(nestedKey, "$") + "\"does not exist in the options!").c_str());

There doesn't seem to be a newer jasp to bump to, so we could disable format security for the moment. @TomaSajt

Sage is blocked by python3Packages.rpy2, which is failing using 3.11 during testing due to a segfault. This segfault does not happen with python 3.12. Any suggestions @joelmo? Sage builds fine when disabling tests so this is the only problem to resolve for sage.

[TomaSajt]

For jasp-desktop I guess we could just do

env.NIX_CFLAGS_COMPILE = "-Wno-error=format-security";

I think it's fine to include it in this PR.

[collares]

@jbedo If I understand correctly, the CI runs at rpy2/rpy2#1051 segfault on the same test (test_embedded_r.py) running under Python 3.12, which is consistent with the undefined behavior explanation.

[jbedo]

That's great sluthing, and good to know it isn't resolved with 3.12. I'll spend some time trying to get the ABI mode to work.

[collares]

Actually, I am not sure the ABI suggestion definitely helps. If you run the minimized tastcase under valgrind --trace-children=yes, both the ABI and the API mode report invalid reads when invoking callbacks. But it might be a good enough workaround while we wait for an upstream fix.

In fact, the same valgrind errors show up at 5b706ee, which is the first Nixpkgs commit at which rpy2 builds under Python 3.10 (I can't check Python 3.9 and below, because the valgrind output is a lot messier even for good Python scripts).

Edit: I think using R_tryCatchError with Python callbacks as rpy2 does is just broken, regardless of {Python, cffi, R, rpy2} version. See rpy2/rpy2#1111 (comment) for more details.

[jbedo]

I'm unsure as to the best way forward: this bug really needs to be fixed upstream. Changing ABI/hardening/optimisation really does nothing, we just sidestep the bug during the test case with some luck. Is this any better than disabling tests? rpy2 is also still broken with the old R 4.3.3 version as you've discovered, so there doesn't seem to be much point to holding the R version bump back waiting for a fix and we may as well pick one of these options and then update rpy2 when an upstream fix is available.

[collares]

Sure, I'm happy with something like disabledTests = [ "test_parse_incomplete_error" "test_parse_error" "test_parse_error_when_evaluating" ];, along with a link to the rpy2 issue. Thanks!

Edit: ofBorg is happy.

[collares]

@ofborg build sageWithDoc

[b-rodrigues]

R 4.4.1 got released last week, what shall we do, merge this one and re-bump, or directly bump to 4.4.1?

[jbedo]

R 4.4.1 got released last week, what shall we do, merge this one and re-bump, or directly bump to 4.4.1?

I'm planning to bump to 4.4.1, just preparing it and checking it. It should be a fairly minor change since we already got 4.4.0 in good shape.

[jbedo]

49 packages built:
R R.tex cantor diffoscope diffoscope.dist diffoscope.man jasp-desktop jetbrains.dataspell labplot ocamlPackages.ocaml-r postgresql12JitPackages.plr postgresql12Packages.plr postgresql13JitPackages.plr postgresql13Packages.plr postgresql14JitPackages.plr postgresql14Packages.plr postgresql15JitPackages.plr postgresql15Packages.plr postgresql16JitPackages.plr postgresql16Packages.plr python311Packages.cnvkit python311Packages.cnvkit.dist python311Packages.radian python311Packages.radian.dist python311Packages.rchitect python311Packages.rchitect.dist python311Packages.rpy2 python311Packages.rpy2.dist python312Packages.cnvkit python312Packages.cnvkit.dist python312Packages.radian python312Packages.radian.dist python312Packages.rchitect python312Packages.rchitect.dist python312Packages.rpy2 python312Packages.rpy2.dist quarto rWrapper radianWrapper resorter rstudio rstudio-server rstudioServerWrapper rstudioWrapper sage sageWithDoc
spark spark_3_4 vscode-extensions.reditorsupport.r

[b-rodrigues]

I don't see any other major packages that must absolutely be fixed, so for me this can be merged!