[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]

[Andreas Tille]

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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