[Debian-med-packaging] C++ help needed for psortb

[Andreas Tille]

Hi Bastien,

On Wed, Apr 19, 2017 at 01:32:43PM +0000, Bastien Roucaries wrote:
> 
> Le 19 avril 2017 08:09:11 GMT+02:00, Andreas Tille <andreas at an3as.eu> a écrit :
> >
> >Psortb[1] was using header files from biosquid[2] and hmmer2[3] but did
> >not shipped the according library code.  No idea how this might have
> >worked - I assume most users just took the compiled binaries and did
> >not
> >noticed.  Biosquid and hmmer2 development is discontinued.  There is
> >hmmer 3.x but several users rely on hmmer2.  The latter contained
> >another copy of biosquid which I removed inside the package in
> >experimental by dynamically linking against biosquid.  The biosquid
> >package in experimental was also overhauled with newly written automake
> >stuff to enable dynamic libraries which were not available before.
> >
> >In other words: The biosquid library is used by two packages (hmmer2
> >and
> >psortb - possibly more code copies around which will be removed later)
> >but as far as I know hmmer2 was creating the library only to link its
> >own executables.  While I'd prefer a dynamic library for the same
> >reasons as you specified above the effort to realise this is higher and
> >the use less than for biosquid (but I would not stop anybody to invest
> >some time into low popcon orphaned code which is not bad in principle)
> 
> Could you please give some string ti identify both library ? 

I'm sorry, I can't parse this.  Current status is:  With Build-Depends

               libsquid-dev (>= 1.9g+cvs20050121-9~),
               libhmmer2-dev (>= 2.3.2+dfsg-2~),

the build target of psortb succeeds but package build fails in
build time test due to missing symbol:

#     Error:  Can't load '/build/psortb-3.0.4+dfsg/bio-tools-psort-svmloc/../blib/arch/auto/Bio/Tools/PSort/SVMLoc/SVMLoc.so' for module Bio::Tools::PSort::SVMLoc: /build/psortb-3.0.4+dfsg/bio-tools-psort-svmloc/../blib/arch/auto/Bio/Tools/PSort/SVMLoc/SVMLoc.so: undefined symbol: _ZN7DataSet12getAttributeEi at /usr/lib/x86_64-linux-gnu/perl/5.24/DynaLoader.pm line 187.


So what "string to identify both libraries" do you want me to give to
approach what?

Kind regards

      Andreas.
 
> >[1] https://anonscm.debian.org/git/debian-med/psortb.git
> >[2] https://anonscm.debian.org/git/debian-med/biosquid.git
> >[3] https://anonscm.debian.org/git/debian-med/hmmer2.git

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