[Debian-med-packaging] Solved (Was: Problems building psortb from source)

[Andreas Tille]

Hi,

just to let you know.  I think I've found the solution which seems to
be that I also need

   http://www.psort.org/download/libpsortb-1.0.tar.gz

When building this lib I can link psortb against it.  I admit I was
confused since the psortb download has the term 'all' inside the tarball
name and several duplicated files with the lib download.  It might make
sense to express this issue more clearly.

Sorry for the noise

       Andreas.

On Sat, Apr 22, 2017 at 08:08:25AM +0200, Andreas Tille wrote:
> 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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> http://fam-tille.de
> 
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