[Debian-med-packaging] Bug#963774: mcl breaks roary autopkgtest: Cannot find the mcxdeblast executable, please ensure its in your PATH

[hello]

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