[Debian-med-packaging] Psortb has errors in Perl testsuite

[Carnë Draug]

On 19 April 2017 at 16:06, Andreas Tille <tille at debian.org> wrote:
> Hi Carnė,
>
> On Wed, Apr 19, 2017 at 03:52:30PM +0100, Carnė Draug wrote:
>> >
>> > I think I found the problem.  DataSet::getAttribute(int) is defined in
>> > bio-tools-psort-svmloc/libsvm.cpp.  While
>> > [...]
>>
>> The filename rang a bell and seems like they are vendorising libsvm
>> [1].  This is confirmed on the README file inside the
>> bio-tools-psort-svmloc directory:
>>
>>   Algorithm::SVM is based on the libsvm 2.8 library written by
>>   Chih-Chung Chang and Chih-Jen Lin.
>>
>> Turns out that psortb is actually vendorising Algorithm::SVM [2] (they
>> just moved it out of the Algorithm::SVM namespace and into
>> Bio::Tools::PSort::SVMLoc) which in turn is vendorising libsvm.  My
>> understanding of Debian packaging is that such things should be
>> removed, packaged as separate, and made as dependencies.
>
> I confirm that I noticed that this is a code copy of libsvm but Debian
> has libsvm-3.21 and when I checked the package source of libsvm I came
> to the conclusion that the code copy is different enough from what
> Debian is distributing to get into even more trouble than I'm currently
> observing.
>
> I can confirm that I understood [3] and try to do my best (and thus
> removing code copies of biosquid and hmmer2) but I in this case I do not
> see any advantage of separate packaging.
>
> Kind regards and thanks for the hint anyway
>
>       Andreas.
>
>> [1] https://www.csie.ntu.edu.tw/~cjlin/libsvm/
>> [2] https://metacpan.org/pod/Algorithm::SVM
>> [3] https://wiki.debian.org/UpstreamGuide#No_inclusion_of_third_party_code
>

Seems like some people from Fedora have faced the same issue and
already solved it for you.  They sent their patch upstream [4]
although it seems like the current maintainer does not reply to bugs,
or at least not the ones reported on RT [5].  There was one other
issue that may be important too about being able to build for 32 bit
with recent versions of perl [6].

Carnë

[4] https://rt.cpan.org/Public/Bug/Display.html?id=79106
[5] https://rt.cpan.org/Public/Dist/Display.html?Name=Algorithm-SVM
[6] https://rt.cpan.org/Public/Bug/Display.html?id=79754