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Re: psortb, libalgorithm-svm-perl, and other missing dependencies

On 15 July 2017 at 13:57, Carnë Draug <carandraug+dev@gmail.com> wrote:
> On 15 July 2017 at 06:52, Andreas Tille <andreas@an3as.eu> 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


[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

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