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From: "Ludovic Courtès" <ludo@gnu.org>
To: Felix Gruber <felgru@posteo.net>
Cc: 50813-done@debbugs.gnu.org
Subject: bug#50813: [PATCH] gnu: python-pandas: Update to 1.3.3.
Date: Tue, 12 Oct 2021 16:52:13 +0200	[thread overview]
Message-ID: <87lf2yuwgy.fsf_-_@gnu.org> (raw)
In-Reply-To: <20211010150434.1966-1-felgru@posteo.net> (Felix Gruber's message of "Sun, 10 Oct 2021 15:04:28 +0000")

Hi Felix,

Felix Gruber <felgru@posteo.net> skribis:

> On 10/7/21 11:07 AM, Ludovic Courtès wrote:
>> 
>> Felix Gruber <felgru@posteo.net> skribis:
>> 
>>> * gnu/packages/python-science.scm (python-pandas): Update to 1.3.3.
>> 
>> The upgrade appears to cause build failures for python-dask and
>> pigx-rnaseq (via snakemake) among other things.
>> 
>> Could you take a look?
>
> I could not reproduce the build failure in pigx-rnaseq. For python-dask
> the build failure could be fixed by upgrading it to 2021.9.1, whose
> changelog mentioned that they've deactivated a failing test when
> building against Pandas >= 1.3.3. After updating dask, its dependent
> packages python-distributed and python-eliot failed to build.  I've
> fixed both by updating them to their latest releases and disabling
> failing tests.
> I've also took the oppurtunity to update the synapse package which was
> the only package depending on python-eliot.

Neat.

>> For the record, I tried to build everything reported by ‘guix refresh -l
>> python-pandas’ though some of them (ocaml4.07-re, etc.) would already
>> fail to build before the upgrade.
>
> Of the remaining packages reported by `guix refresh -l python-pandas`,
> I've identified the following packages with build failures:
>
> * clipper@2.0
>   sometimes fails due to nondeterministic test
>   `test_get_FDR_cutoff_mean`.  The docstring of this test already says
>   "Difficult to test because of random sampling" followed by a TODO.
>   I've thus deactivated this test, to make it build deterministically.
> * pplacer@1.1.alpha19
>   already failed on master due to unbuildable ocaml4.07-re@1.10.3.
> * python-scikit-rebate@0.6
>   Already failed on master in test `skrebate`:
>   ModuleNotFoundError: No module named 'sklearn.externals.joblib'
>   (A guix refresh -u python-scikit-rebate would update it to 0.62 which
>    was buildable, but this version seemed to come without any tests, so
>    I'm not sure if this is the right solution.)
> * orange@3.28.0
>   Already failed to build on mater, because its dependency
>   python-orange-canvas-core.
>   I've looked into updating both to their latest version, but that
>   would require updating python-pygments to >= 2.8.0 which would entail
>   rebuilding 561 dependent packages.
> * imp@2.13.0
>   I was running out of memory while building imp, which in the end
>   killed the build process. It seems that my 8GB of RAM are not
>   sufficient to build imp, so I cannot tell if the update of
>   python-pandas might break imp.
> * tadbit@1.0.1
>   depends on imp, so I couldn't build it either.
>
> I've prepared patches for those packages that I was able to fix.

Awesome.

>   gnu: python-pandas: Update to 1.3.3.
>   gnu: python-dask: Update to 2021.9.1.
>   gnu: python-distributed: Update to 2021.09.1.
>   gnu: python-eliot: Update to 1.13.0.
>   gnu: synapse: Update to 1.44.0.
>   gnu: clipper: Disable non-deterministic test.

python-dask and pigx-rnaseq build fine for me with this patch series,
along with everything in between.

Applied, thank you!

Ludo’.




  parent reply	other threads:[~2021-10-12 14:53 UTC|newest]

Thread overview: 15+ messages / expand[flat|nested]  mbox.gz  Atom feed  top
2021-09-26  9:47 [bug#50813] [PATCH] gnu: python-pandas: Update to 1.3.3 Felix Gruber
2021-10-07  9:07 ` Ludovic Courtès
2021-10-10 15:04   ` [bug#50813] [PATCH v2 0/6] " Felix Gruber
2021-10-12 13:28     ` Greg Hogan
2021-10-12 14:52     ` Ludovic Courtès [this message]
2021-10-10 15:04   ` [bug#50813] [PATCH v2 1/6] " Felix Gruber
2021-10-10 15:04   ` [bug#50813] [PATCH v2 2/6] gnu: python-dask: Update to 2021.9.1 Felix Gruber
2021-10-10 15:04   ` [bug#50813] [PATCH v2 3/6] gnu: python-distributed: Update to 2021.09.1 Felix Gruber
2021-10-10 15:04   ` [bug#50813] [PATCH v2 4/6] gnu: python-eliot: Update to 1.13.0 Felix Gruber
2021-10-10 15:04   ` [bug#50813] [PATCH v2 5/6] gnu: synapse: Update to 1.44.0 Felix Gruber
2021-10-13 12:01     ` Michael Rohleder
2021-10-13 16:33       ` Felix Gruber
2021-10-14  4:25         ` Michael Rohleder
2021-10-14 19:08           ` Felix Gruber
2021-10-10 15:04   ` [bug#50813] [PATCH v2 6/6] gnu: clipper: Disable non-deterministic test Felix Gruber

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