On 25 July 2017 at 21:18, Andreas Tille <[email protected]> wrote: > Hi Carnė, > > On Tue, Jul 25, 2017 at 04:22:07PM +0100, Carnė Draug wrote: >> > >> > These tests are ran against the installed package and not during the >> > build. I just call autopkgtest with the changes file after the >> > build. The setup instructions are on the pkg-perl page [1] >> > >> > Carnė >> > >> > [1] https://pkg-perl.alioth.debian.org/autopkgtest.html#SETUP >> >> I went to try and fix this and found some missing dependencies which >> are still not packaged in Debian. >> >> One is an Apache module which I have no idea where it comes from. It >> is used on the server startup.pl [2]. >> >> Another is XML::RPC [3] which is also not packaged in Debian. >> >> Then there is Bio::PSort::ModuleI [4] which is not part of their >> release. I think they probably meant to use >> Bio::Tools::PSort::ModuleI instead. >> >> In addition, I got a bunch of redefined symbols and 'my $variables' >> masking previous declarations warnings. >> >> I didn't look any further than this, other issues may pop up after >> fixing those. > > Thanks a lot for your investigation. It is really appreciated since > I'm currently quite flooded with work. > >> I tried to push one change but I don't have push access to debian-med >> repositories. > > I've added you to the Debian Med team so you should be able to push. >
I have pushed the one change I made which was adding some missing dependencies. I could package one other missing dependency, XML::RPC, but feels like a whack-a-mole. I cloned libpsortb which has libsvmloc and that had problems too. The issue I had with libsvm was that libsvmloc.so was not linked against svm, and indeed, the package build shows this warnings: dpkg-shlibdeps: warning: symbol svm_predict used by debian/libsvmloc0/usr/lib/x86_64-linux-gnu/libsvmloc.so.0.0.0 found in none of the libraries dpkg-shlibdeps: warning: symbol svm_load_model used by debian/libsvmloc0/usr/lib/x86_64-linux-gnu/libsvmloc.so.0.0.0 found in none of the libraries I believe that's because the patch used uses LDADD to add the -lsvm flag. However, LDADD is only used for programs, not shared libraries and so gets ignored. I believe the right automake incantation is either: libsvmloc_la_LIBADD = -lsvm or just append it to the existing libsvmlov_la_LDFLAGS. Probably the later. However, when I tried to build this, I would get an error: devlibs error: There is no package matching [libsvm3-dev] and noone provides it, please report bug to d-shlibs maintainer debian/rules:11: recipe for target 'override_dh_auto_install' failed make[1]: *** [override_dh_auto_install] Error 1 make[1]: Leaving directory '/build/libpsortb-1.0+dfsg' debian/rules:8: recipe for target 'binary' failed make: *** [binary] Error 2 dpkg-buildpackage: error: fakeroot debian/rules binary gave error exit status 2 and I guess that's me not knowing enough about how the Debian packaging works. Carnë
