Hi Shayan, it seems make is not traversing src/alien/oxygen to install the said tool (and the other one mclblastline) as well as its manpages. I created 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 have different 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/mcxdeblast Control 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# make make[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 && make the manpages will be build and cd src/alien/oxygen/src && make install does an installation to /usr/local/bin. So the way to re-add the missing files manually seems to be clear. But I wonder why this was not needed in version 1:14-137+ds-4. Since you worked intensely on the mcl package recently you might have an idea for a 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...@lists.debian.org > User: debian...@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-packag...@alioth-lists.debian.net > https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-packaging -- http://fam-tille.de