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 <cjfiel...@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" <andr...@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 < > nore...@release.debian.org> ----- > > Date: Mon, 30 Mar 2020 04:39:17 +0000 > From: Debian testing autoremoval watch <nore...@release.debian.org> > To: bioperl-...@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 > > > _______________________________________________ > Debian-med-packaging mailing list > debian-med-packag...@alioth-lists.debian.net > > https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-packaging > > ----- End forwarded message ----- > > -- > http://fam-tille.de > > > ᐧ
