[Debian-med-packaging] Problems building psortb from source (Re: Psortb has errors in Perl testsuite)

[Andreas Tille]

Hi psortb developers,

I'm writing you on behalf of the Debian Med team which is a group of
Debian developers with the objective to package Free Software in live
sciences and medicine for official Debian.  Since I received a user
request to package psortb.

When trying to build psortb I worked around issues caused by the fact
that there were some incompatibilities with Debian packaged biosquid and
hmmer2 (from the latter also some code seems to be missing in case you
want to avoid linking to external library from hmmer2 I doubt psortb can
be built successfully).  If you are interested in this you can have a
look at the according discussion on the Debian Med development list[1].
To implement this I have applied some patches to the packaging[2].

Unfortunately there is a hurdle remaining we were not able to take since
it seems there is some code missing.  It seems that the file
bio-tools-psort-svmloc/bindings.cpp.  This is discussed in a thread on
the Debian Med developer list[3] - I quoted the most informative mail
below.

We found out that you are using a fork of Algorithm::SVM which somehow
looks to divergent to replace it by the original Algorithm::SVM but some
code parts are missing and it does not build.  It would help if you
would clarify the motivation for this fork and if it is really needed
we somehow need some hints how to build it successfully.

Kind regards

      Andreas.

[1] https://lists.alioth.debian.org/pipermail/debian-med-packaging/2017-April/051686.html
[2] https://anonscm.debian.org/cgit/debian-med/psortb.git/tree/debian/patches
[3] https://lists.alioth.debian.org/pipermail/debian-med-packaging/2017-April/051746.html
[4] https://metacpan.org/release/Algorithm-SVM

On Thu, Apr 20, 2017 at 08:25:44PM +0100, Carnë Draug wrote:
> On 20 April 2017 at 19:41, Carnë Draug <carandraug+dev at gmail.com> wrote:
> > [...]
> > I noticed that there is no `bio-tools-psort-svmloc/bindings.cpp` file,
> > there is only `bio-tools-psort-svmloc/bindings.h`.  I couldn't find
> > the definitions of the DataSet and SVM classes declared in bindings.h.
> > Maybe that is part of the issue?
> >
> 
> I have attached a patch that removes the bundled libsvm from psortb.
> 
> However, the code was originally using libsvm2 while Debian packages
> libsvm3.  But that libsvm version specific code should have been in
> the bindings.cpp file which is missing in psortb so I can't fix that.
> If the file was there, the fix should be similar to this patch in
> libalgorithm-svm-perl [1].
> 
> Carnë
> 
> [1] https://anonscm.debian.org/cgit/pkg-perl/packages/libalgorithm-svm-perl.git/tree/debian/patches/update-libsvm3.patch


-- 
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