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rPackages.ExomeDepth 1.1.15 : error: expected ';' before 'extern' in mathcalls.h #187113

Closed apraga closed 1 year ago

apraga commented 2 years ago

Steps To Reproduce

Steps to reproduce the behavior:

  1. nix build nixpkgs#rPackages.ExomeDepth

Build log

https://gist.github.com/apraga/2b944b217226553759ae94379e13547e

Additional context

What I don’t understand is that only the macro after #if defined __USE_XOPEN_EXTENDED || defined __USE_ISOC99 fails, even though the syntax is similar. I’ve tried to compile with -std=c11, but to no avail.

Notify maintainers

@jbedo

Metadata

Please run nix-shell -p nix-info --run "nix-info -m" and paste the result.

[user@system:~]$ nix-shell -p nix-info --run "nix-info -m"
 - system: `"x86_64-linux"`
 - host os: `Linux 5.10.16.3-microsoft-standard-WSL2, Ubuntu, 20.04.4 LTS (Focal Fossa), nobuild`
 - multi-user?: `no`
 - sandbox: `yes`
 - version: `nix-env (Nix) 2.10.3`
 - channels(apraga): `"nixpkgs"`
 - nixpkgs: `/home/apraga/.nix-defexpr/channels/nixpkgs`
jbedo commented 2 years ago

This is working in 22.05 so something in the toolchain has changed. Should be able to bisect this and figure it out.

jbedo commented 2 years ago

Well that took a while but it did isolate the issue to this commit:

commit 272fc53af162d1e4619d03987bc0701ec12d5df7
Author: Bernardo Meurer <bernardo@meurer.org>
Date:   Fri Jul 22 22:30:56 2022 -0700

    glibc: 2.34-210 -> 2.35-163

Looks like the package is not compatible with glibc 2.35.

apraga commented 2 years ago

Thanks for the quick answer. So the update did not triggered a new build of ExomeDepth ? Also, is there a way to patch this ?

jbedo commented 2 years ago

We don't build rPackages regularly, only on the r-updates branch which hasn't had a bump for a while now. Need to look further into it and see if upstream are aware.

apraga commented 2 years ago

@jbedo Did you have time to look into this issue ? It does not seem to be solved on my end. Thanks !

jbedo commented 1 year ago

This seems to be fixed in ExomeDepth 1.1.16, which will be part of nixpkgs once we bump R to 4.2.2 (and pull in the latest CRAN). In the meantime you can override ExomeDepth and point it to the 1.1.16 source tarball.

abathur commented 1 year ago

Closing since the update to 1.1.16 was added in #206157 which has been available in unstable for a while and should also be present in the 23.05 as soon as it's officially released.

Happy to reopen if I'm mistaken. @apraga are you able to confirm?

apraga commented 1 year ago

With latest unstable, it does compile. Thanks @abathur .