[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]

[Christopher Fields]

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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