[Debian-med-packaging] Bug#954511: Can someone habe a look at bioperl-run in connection with kalign (was: bioperl-run is marked for autoremoval from testing]

[Pranav Ballaney]

Hi,
Yes, Kalign is on v3 now.
I've pushed some patches to fix this bug. All build-time tests pass now.
Autopkgtests don't, however, but that issue seems to be unrelated.
Please take a look at https://salsa.debian.org/med-team/bioperl-run and
verify the patches. This is my first time working with quilt patches so
apologies if I did something wrong.

Regards,
Pranav

On Mon, Mar 30, 2020 at 8:23 PM Christopher Fields <cjfields1 at gmail.com>
wrote:

> I have seen per exit codes of 256 for other bioperl-run wrappers in the
> past where the application API changed (constant game of playing catchup
> unfortunately).  That seems to be the case here based on the error.   Is
> kalign is now at v3?
>
> chris
>
> On 3/30/20, 2:57 AM, "Andreas Tille" <andreas at an3as.eu> wrote:
>
>     Control: tags -1 help
>
>     Hi,
>
>     currently bioperl-run fails.  I think the issue is:
>
>
>     > #   Failed test 'Code tested only on kalign versions >= 2'
>     > #   at t/Kalign.t line 23.
>     > #          got: ''
>     > #     expected: '1'
>     > [2020-03-22 03:18:02] :   ERROR : Input alignment format could not
> be detected. (rwalign.c line 314)
>     > [2020-03-22 03:18:02] :   ERROR : Function
> "detect_alignment_format(b, &type)" failed. (rwalign.c line 187)
>     > [2020-03-22 03:18:02] :   ERROR : Function "tmp_msa =
> read_input(param->infile[i],tmp_msa)" failed. (run_kalign.c line 383)
>     > [2020-03-22 03:18:02] :   ERROR : Function "run_kalign(param)"
> failed. (run_kalign.c line 353)
>     >
>     > --------------------- WARNING ---------------------
>     > MSG: Kalign call crashed: 256 [command /usr/bin/kalign -in
> t/data/cysprot.fa  -out /tmp/ilV8fEWBHj/nJrv_GQaDU]
>
>
>     but please double check.  Could someone have a look please?
>
>     Kind regards
>
>            Andreas.
>
>     ----- Forwarded message from Debian testing autoremoval watch <
> noreply at release.debian.org> -----
>
>     Date: Mon, 30 Mar 2020 04:39:17 +0000
>     From: Debian testing autoremoval watch <noreply at release.debian.org>
>     To: bioperl-run at packages.debian.org
>     Subject: bioperl-run is marked for autoremoval from testing
>
>     bioperl-run 1.7.3-3 is marked for autoremoval from testing on
> 2020-05-05
>
>     It is affected by these RC bugs:
>     954511: bioperl-run: FTBFS: dh_auto_test: error: perl Build test
> --verbose 1 returned exit code 255
>
>
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>
>     --
>     http://fam-tille.de
>
>
> ᐧ
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