Re: Can someone habe a look at bioperl-run in connection with kalign (was: bioperl-run is marked for autoremoval from testing]
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@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@release.debian.org> -----
Date: Mon, 30 Mar 2020 04:39:17 +0000
From: Debian testing autoremoval watch <noreply@release.debian.org>
To: bioperl-run@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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