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

[Andreas Tille]

Hi Carnë,

On Wed, Apr 19, 2017 at 03:52:30PM +0100, Carnë 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

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