IRC channel logs

<rekado>it’s a new channel with almost all Bioconductor packages

<rekado>civodul: could you please add a jobspec for guix-bioc to guix.bordeaux.inria.fr? It’s <2000 new R packages.

<rekado>the channel lives at https://github.com/guix-science/guix-bioc and depends on guix-cran.

<civodul>coming soon: https://guix.bordeaux.inria.fr/jobset/guix-bioc

<civodul>great that you managed to come up with this channel!

<civodul>no need for BioConda or Biowhatever now :-)

<civodul>rekado: it’d be great if you could add it at https://git.savannah.gnu.org/cgit/guix/maintenance.git/tree/hydra/bayfront.scm#n125 (in two places) for hpc.guix.info/channels knows about it

<civodul>it’s broken: https://guix.bordeaux.inria.fr/eval/7403535/log/raw

<rekado>ah

<rekado>weird because we’re using “guix pull” to check that it’s fine

<rekado>not sure what the error means, but the package in question has this list of inputs: (inputs (list python-scikit-learn python packaging))

<rekado>and “packaging” looks wrong

<rekado>that should be python-packaging

<rekado>I’ll update the importer

<rekado>but I wonder why this wasn’t removed as a bad input

<rekado>will fix it later tonight

<rekado>civodul: thanks for adding it

<rekado>once it’s fixed I’ll add it to bayfront.scm

<civodul>awesome

<civodul>rekado: it’s building! \o/

<civodul> https://guix.bordeaux.inria.fr/jobset/guix-bioc

<rekado>yay

<rekado>I’m not confident that it will remain in a buildable status. I think there still is a bug in the channel generator script.

<rekado>I’ll try to get around to it soon

<civodul>pretty nice anyway

<civodul>we should claim biocontainer.org and have a ‘guix pack’ web frontend

<rekado>hah!

<rekado>status: REG REQUESTED

<rekado>it’s a good idea

<civodul>ACTION looks at https://docs.gitlab.com/16.7/ee/ci/pipelines/merge_trains.html#enable-merge-trains with envy

<rekado>I’m trying to fix python2-scipy in guix-past

<rekado>this is the error: ImportError: /gnu/store/w2xy0r1gbccb8xlma40xznbhakc63wh0-python2-scipy-1.2.3/lib/python2.7/site-packages/scipy/special/_ufuncs_cxx.so: undefined symbol: expl, version GLIBCXX_3.4

<rekado>this library is linked with libm and libm contains expl. Is it about the symbol version?

<rekado>“nm -gD /gnu/store/qzqq7za0mqvxgp7q8jmzd97c22xbqd18-gcc-7.5.0-lib/lib/libstdc++.so.6 | grep expl” says that we have “00000000000ae820 T expl@@GLIBCXX_3.4”

<rekado>and _ufuncs_cxx.so is in fact linked with that libstdc++.so.6

<rekado>any ideas?

<rekado>(we only get this error when manually importing; the build log only claims that it “cannot import name _ufuncs”)

<civodul>gcc-7.5.0?

<civodul>could it be a mismatch with the default gcc (11.x)?

<rekado>good idea!

IRC channel logs

2024-01-18.log