Re: [help] vdjtools autopkgtest fails

Hi Andreas, Le 27/11/2022 à 07:07, Andreas Tille a écrit : Hi Pierre, when fixing the watch file I stumbled upon an autopkgtest error[1]. Do you have an idea what might be wrong here? At last I found classpath issues in the build, and I could provide a cleaner way to build the jar which was

Re: Help for unifrac autopkgtest needed

Hi Étienne, Am Sat, Dec 03, 2022 at 10:46:26PM +0100 schrieb Étienne Mollier: > > Probably nothing outstanding, liblapacke introduced the ztrsyl3_ > in its version 3.11 and unifrac built against that, but the test > might have run against liblapacke 3.10 in testing which didn't > have this symbal

[Advent bug squashing] Re: PIQUE

Hi Tony, Am Sun, Dec 04, 2022 at 01:39:40AM + schrieb Tony Travis: > Thanks for creating the "pique" package for my GWAS pipeline. I've just > installed it under Ubuntu 22.04 LTS and it installed quite a lot of > packages, but fails to run my tests with the error: > > > Error in library(multt

PIQUE

Hi, Andreas. Thanks for creating the "pique" package for my GWAS pipeline. I've just installed it under Ubuntu 22.04 LTS and it installed quite a lot of packages, but fails to run my tests with the error: Error in library(multtest) : there is no package called ‘multtest’ I'll file a BUG re

Re: Help for unifrac autopkgtest needed

Hi Andreas, Andreas Tille, on 2022-12-01: > ImportError: /lib/x86_64-linux-gnu/liblapacke.so.3: undefined symbol: ztrsyl3_ […] > Any idea what might be wrong here? Probably nothing outstanding, liblapacke introduced the ztrsyl3_ in its version 3.11 and unifrac built against that, but the test mig

[Advent bug squashing] fixed bug #1018533 in python-mne

A last one for today, python-mne might need quite some more attention (newer upstream releases, a number of lintian errors), but at least there's one less case of nose usage in packages. Have a nice day, :) -- Étienne Mollier Fingerprint: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da Sent

[Advent bug squashing] fixed bug #1018551 in python-pbcore

bug #1018551 in python-pbcore was yet another instance of nose replacement by pytest. Have a nice day, :) -- Étienne Mollier Fingerprint: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da Sent from /dev/pts/2, please excuse my verbosity. On air: Saga - The Interview signature.asc Descriptio

Re: [Advent bug squashing] fixed bug #1018377 in insilicoseq

Hi Bilal, insilicoseq is uploaded with a minor change to silence runtime-test-file-uses-supported-python-versions-without-test-depends (yeah that's a hell of a lintian warning). Thank you for your contributions! Have a nice day, :) -- Étienne Mollier Fingerprint: 8f91 b227 c7d6 f2b1 948c 823

Re: [Advent bug squashing] fixed bug #1018377 in insilicoseq

On 12/4/22 00:53, Étienne Mollier wrote: I'm under the impression I'm missing the commit. Oops, sorry ! I forgot to `git push`. Done that now. Thanks :) -- Mohammed Bilal 2D65 BC1E B966 5A6E 97F9 730A B3F5 9452 8521 9E1F OpenPGP_signature Description: OpenPGP digital signature

Re: [Advent bug squashing] fixed bug #1018377 in insilicoseq

Hi Bilal, Mohd Bilal, on 2022-12-04: > On 12/3/22 23:50, Étienne Mollier wrote: > > test_ncbi needs to be skipped. > > Done. Thanks for spotting this :) I still see the test failing on my end, did I miss something? I'm under the impression I'm missing the commit. > Also can you take a look at p

Re: [Advent bug squashing] fixed bug #1018377 in insilicoseq

On 12/3/22 23:50, Étienne Mollier wrote: [..] test_ncbi needs to be skipped. Done. Thanks for spotting this :) Also can you take a look at python-biom-format[2]. I've pushed a fix for #1018464. The fix was a simple one (remove depends on nose). Upstream already uses pytest. Someone probabl

[Advent bug squashing] fixed bug #1018559 in python-pyani

Upstream python-pyani is moving away of nosetests already, so the patching might have been a bit overkill, but the bug is closed nevertheless. Have a nice day, :) -- Étienne Mollier Fingerprint: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da Sent from /dev/pts/2, please excuse my verbosity

Re: [Advent bug squashing] fixed bug #1018377 in insilicoseq

Hi Bilal, Mohd Bilal, on 2022-12-03: > I just pushed a a fix for porting insilicoseq's test to pytest. I would > request someone from the team to take a look and sponsor my changes I have reviewed through your changes, and they look even better than what I think I might have wrapped up. There is

[Advent bug squashing] fixed bug #1018377 in insilicoseq

Hello team, I just pushed a a fix for porting insilicoseq's test to pytest. I would request someone from the team to take a look and sponsor my changes [1] - https://salsa.debian.org/med-team/insilicoseq Thanks :) -- Mohammed Bilal 2D65 BC1E B966 5A6E 97F9 730A B3F5 9452 8521 9E1F OpenPGP_s

[Advent bug squashing] fixed bug #1018565 in python-pymummer

python-pymummer didn't require upstream code patching to proceed to the migration to pytest. :) There may be others; I'm going through the list from newer entry to older. Have a nice day, :) -- Étienne Mollier Fingerprint: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da Sent from /dev/pts

[Advent bug squashing] fixed bug #1018582 in python-sqt

Good day, I migrated python-sqt test engine from nose to pytest. The patch is, for once, in good enough shape to be merged upstream, but I lacked the patience to deal with bitbucket, if there are takers… Have a nice day, :) -- Étienne Mollier Fingerprint: 8f91 b227 c7d6 f2b1 948c 8236 793c