<html><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"></head><body dir="auto"><div dir="auto">Hello Andreas, </div><div dir="auto"><br></div><div dir="auto">That's very strange. I will see if I can reproduce this from what you've said and find a solution to it tomorrow. </div><div dir="auto"><br></div><div dir="auto">Kind regards, </div><div dir="auto">Shayan Doust</div><div dir="auto"><br></div><div><br></div><div style="font-size:100%;color:#000000" dir="auto"><!-- originalMessage --><div>-------- Original message --------</div><div>From: Andreas Tille <tille@debian.org> </div><div>Date: 27/06/2020 07:11 (GMT+00:00) </div><div>To: Paul Gevers <elbrus@debian.org>, 963774@bugs.debian.org, Shayan Doust <hello@shayandoust.me> </div><div>Subject: Re: Bug#963774: mcl breaks roary autopkgtest: Cannot find the
mcxdeblast executable, please ensure its in your PATH </div><div><br></div></div>Hi Shayan,<br><br>it seems make is not traversing src/alien/oxygen to install the said<br>tool (and the other one mclblastline) as well as its manpages. I<br>created the debdiff with the version in testing:<br><br>$ debdiff mcl_1%3a14-137+ds-4_amd64.deb mcl_1%3a14-137+ds-7_amd64.deb <br>[The following lists of changes regard files as different if they have<br>different names, permissions or owners.]<br><br>Files in first .deb but not in second<br>-------------------------------------<br>-rw-r--r-- root/root /usr/share/man/man1/mclblastline.1.gz<br>-rw-r--r-- root/root /usr/share/man/man1/mcxdeblast.1.gz<br>-rwxr-xr-x root/root /usr/bin/mclblastline<br>-rwxr-xr-x root/root /usr/bin/mcxdeblast<br><br>Control files: lines which differ (wdiff format)<br>------------------------------------------------<br>Depends: libc6 (>= [-2.14)-] {+2.29)+}<br>Homepage: [-http://micans.org/mcl/-] {+https://micans.org/mcl/+}<br>Installed-Size: [-3986-] {+4509+}<br>Version: [-1:14-137+ds-4-] {+1:14-137+ds-7+}<br><br><br>I admit I don't understand why make does not do anything in<br><br>/build/mcl-14-137+ds/src/alien# make<br>make[1]: Entering directory '/build/mcl-14-137+ds/src/alien'<br>make[1]: Nothing to be done for 'all-am'.<br>make[1]: Leaving directory '/build/mcl-14-137+ds/src/alien'<br><br><br>If I do in the pbuilder chroot<br><br> cd src/alien/oxygen/doc && make<br><br>the manpages will be build and<br><br> cd src/alien/oxygen/src && make install<br><br>does an installation to /usr/local/bin.<br><br>So the way to re-add the missing files manually seems to be clear. But<br>I wonder why this was not needed in version 1:14-137+ds-4. Since you<br>worked intensely on the mcl package recently you might have an idea for<br>a more straightforward fix.<br><br>Kind regards<br><br> Andreas.<br><br>On Fri, Jun 26, 2020 at 08:48:01PM +0200, Paul Gevers wrote:<br>> Source: mcl, roary<br>> Control: found -1 mcl/1:14-137+ds-7<br>> Control: found -1 roary/3.13.0+dfsg-1<br>> Severity: serious<br>> Tags: sid bullseye<br>> X-Debbugs-CC: debian-ci@lists.debian.org<br>> User: debian-ci@lists.debian.org<br>> Usertags: breaks needs-update<br>> <br>> Dear maintainer(s),<br>> <br>> With a recent upload of mcl the autopkgtest of roary fails in testing<br>> when that autopkgtest is run with the binary packages of mcl from<br>> unstable. It passes when run with only packages from testing. In tabular<br>> form:<br>> <br>> pass fail<br>> mcl from testing 1:14-137+ds-7<br>> roary from testing 3.13.0+dfsg-1<br>> all others from testing from testing<br>> <br>> I copied some of the output at the bottom of this report.<br>> <br>> Currently this regression is blocking the migration of mcl to testing<br>> [1]. Due to the nature of this issue, I filed this bug report against<br>> both packages. Can you please investigate the situation and reassign the<br>> bug to the right package?<br>> <br>> More information about this bug and the reason for filing it can be found on<br>> https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation<br>> <br>> Paul<br>> <br>> [1] https://qa.debian.org/excuses.php?package=mcl<br>> <br>> https://ci.debian.net/data/autopkgtest/testing/amd64/r/roary/6058047/log.gz<br>> <br>> autopkgtest [18:20:38]: test test-installed: [-----------------------<br>> Use of uninitialized value in require at<br>> /usr/share/perl5/HTTP/Headers.pm line 302.<br>> Use of uninitialized value in require at<br>> /usr/lib/x86_64-linux-gnu/perl/5.30/Encode.pm line 70.<br>> <br>> Please cite Roary if you use any of the results it produces:<br>> Andrew J. Page, Carla A. Cummins, Martin Hunt, Vanessa K. Wong,<br>> Sandra Reuter, Matthew T. G. Holden, Maria Fookes, Daniel Falush,<br>> Jacqueline A. Keane, Julian Parkhill,<br>> "Roary: Rapid large-scale prokaryote pan genome analysis",<br>> Bioinformatics, 2015 Nov 15;31(22):3691-3693<br>> doi: http://doi.org/10.1093/bioinformatics/btv421<br>> Pubmed: 26198102<br>> <br>> 2020/06/25 18:20:41 Cannot find the mcxdeblast executable, please ensure<br>> its in your PATH<br>> 2,6c2,6<br>> < out/_blast_results<br>> < out/_clustered<br>> < out/_clustered.clstr<br>> < out/_combined_files<br>> < out/_combined_files.groups<br>> ---<br>> > out/accessory.header.embl<br>> > out/accessory.tab<br>> > out/accessory_binary_genes.fa<br>> > out/accessory_binary_genes.fa.newick<br>> > out/accessory_graph.dot<br>> 7a8,18<br>> > out/clustered_proteins<br>> > out/core_accessory.header.embl<br>> > out/core_accessory.tab<br>> > out/core_accessory_graph.dot<br>> > out/gene_presence_absence.Rtab<br>> > out/gene_presence_absence.csv<br>> > out/number_of_conserved_genes.Rtab<br>> > out/number_of_genes_in_pan_genome.Rtab<br>> > out/number_of_new_genes.Rtab<br>> > out/number_of_unique_genes.Rtab<br>> > out/summary_statistics.txt<br>> autopkgtest [18:20:41]: test test-installed: -----------------------]<br>> <br><br><br><br><br>> _______________________________________________<br>> Debian-med-packaging mailing list<br>> Debian-med-packaging@alioth-lists.debian.net<br>> https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-packaging<br><br><br>-- <br>http://fam-tille.de<br></body></html>