On 15 July 2017 at 13:57, Carnë Draug <[email protected]> wrote: > On 15 July 2017 at 06:52, Andreas Tille <[email protected]> wrote: >> On Fri, Jul 14, 2017 at 07:02:58PM +0100, Carnė Draug wrote: >>> [...] >>> I noticed that psortb is now on sid. However, that package seems to >>> be broken. Not only it is missing libalgorithm-svm-perl it seems to >>> be missing a bunch of other dependencies. I have enabled autopkgtest >>> on it [2, 3] which will test each of the modules and will list the >>> missing modules. >> >> Thanks a lot for this. Feel free to commit directly to the packaging >> repository (I took over your commit meanwhile). I'm not that >> comfortable with Perl tests. What would I need to do to run the tests >> as build time test to force the build failing if the test does not pass? >> > > 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] > > Carnë > > [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. I tried to push one change but I don't have push access to debian-med repositories. Carnë [2] https://anonscm.debian.org/cgit/debian-med/psortb.git/tree/psort/server/startup.pl [3] https://anonscm.debian.org/cgit/debian-med/psortb.git/tree/lib/Bio/Tools/PSort/XMLRPC/Client.pm [4] https://anonscm.debian.org/cgit/debian-med/psortb.git/tree/lib/Bio/Tools/PSort/Module/InputI.pm#n58
