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

[Bastien ROUCARIES]

On Wed, Apr 19, 2017 at 4:20 PM, Andreas Tille <tille at debian.org> wrote:
> 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.

I means lintian can detect embeded code. I only need some strings that
reprensent the lib. String is the name of the unix tools.

Bastien
>
>
> 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
>
> --
> http://fam-tille.de