<div dir="ltr"><div dir="ltr" style="user-select: auto;"><div class="gmail_default" style="font-family:arial,helvetica,sans-serif">Hi,</div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif">Yes, Kalign is on v3 now. </div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif">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.<br style="user-select: auto;">Please take a look at <a href="https://salsa.debian.org/med-team/bioperl-run" style="font-family:Arial,Helvetica,sans-serif">https://salsa.debian.org/med-team/bioperl-run</a> and verify the patches. This is my first time working with quilt patches so apologies if I did something wrong. </div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><br style="user-select: auto;"></div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif">Regards,</div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif">Pranav</div></div><br style="user-select: auto;"><div class="gmail_quote" style="user-select: auto;"><div dir="ltr" class="gmail_attr" style="user-select: auto;">On Mon, Mar 30, 2020 at 8:23 PM Christopher Fields <<a href="mailto:cjfields1@gmail.com">cjfields1@gmail.com</a>> wrote:<br style="user-select: auto;"></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">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?<br style="user-select: auto;">
<br style="user-select: auto;">
chris<br style="user-select: auto;">
<br style="user-select: auto;">
On 3/30/20, 2:57 AM, "Andreas Tille" <<a href="mailto:andreas@an3as.eu" target="_blank" style="user-select: auto;">andreas@an3as.eu</a>> wrote:<br style="user-select: auto;">
<br style="user-select: auto;">
Control: tags -1 help<br style="user-select: auto;">
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Hi,<br style="user-select: auto;">
<br style="user-select: auto;">
currently bioperl-run fails. I think the issue is:<br style="user-select: auto;">
<br style="user-select: auto;">
<br style="user-select: auto;">
> # Failed test 'Code tested only on kalign versions >= 2'<br style="user-select: auto;">
> # at t/Kalign.t line 23.<br style="user-select: auto;">
> # got: ''<br style="user-select: auto;">
> # expected: '1'<br style="user-select: auto;">
> [2020-03-22 03:18:02] : ERROR : Input alignment format could not be detected. (rwalign.c line 314)<br style="user-select: auto;">
> [2020-03-22 03:18:02] : ERROR : Function "detect_alignment_format(b, &type)" failed. (rwalign.c line 187)<br style="user-select: auto;">
> [2020-03-22 03:18:02] : ERROR : Function "tmp_msa = read_input(param->infile[i],tmp_msa)" failed. (run_kalign.c line 383)<br style="user-select: auto;">
> [2020-03-22 03:18:02] : ERROR : Function "run_kalign(param)" failed. (run_kalign.c line 353)<br style="user-select: auto;">
> <br style="user-select: auto;">
> --------------------- WARNING ---------------------<br style="user-select: auto;">
> MSG: Kalign call crashed: 256 [command /usr/bin/kalign -in t/data/cysprot.fa -out /tmp/ilV8fEWBHj/nJrv_GQaDU]<br style="user-select: auto;">
<br style="user-select: auto;">
<br style="user-select: auto;">
but please double check. Could someone have a look please?<br style="user-select: auto;">
<br style="user-select: auto;">
Kind regards<br style="user-select: auto;">
<br style="user-select: auto;">
Andreas.<br style="user-select: auto;">
<br style="user-select: auto;">
----- Forwarded message from Debian testing autoremoval watch <<a href="mailto:noreply@release.debian.org" target="_blank" style="user-select: auto;">noreply@release.debian.org</a>> -----<br style="user-select: auto;">
<br style="user-select: auto;">
Date: Mon, 30 Mar 2020 04:39:17 +0000<br style="user-select: auto;">
From: Debian testing autoremoval watch <<a href="mailto:noreply@release.debian.org" target="_blank" style="user-select: auto;">noreply@release.debian.org</a>><br style="user-select: auto;">
To: <a href="mailto:bioperl-run@packages.debian.org" target="_blank" style="user-select: auto;">bioperl-run@packages.debian.org</a><br style="user-select: auto;">
Subject: bioperl-run is marked for autoremoval from testing<br style="user-select: auto;">
<br style="user-select: auto;">
bioperl-run 1.7.3-3 is marked for autoremoval from testing on 2020-05-05<br style="user-select: auto;">
<br style="user-select: auto;">
It is affected by these RC bugs:<br style="user-select: auto;">
954511: bioperl-run: FTBFS: dh_auto_test: error: perl Build test --verbose 1 returned exit code 255<br style="user-select: auto;">
<br style="user-select: auto;">
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</blockquote></div></div><div hspace="streak-pt-mark" style="max-height:1px"><img alt="" style="width:0px;max-height:0px;overflow:hidden" src="https://mailfoogae.appspot.com/t?sender=aYmFsbGFuZXlwcmFuYXZAZ21haWwuY29t&type=zerocontent&guid=b6100cb8-2bda-4b10-ac92-adca5adc5257"><font color="#ffffff" size="1">ᐧ</font></div>