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

[Bastien Roucaries]

Le 19 avril 2017 08:09:11 GMT+02:00, Andreas Tille <andreas at an3as.eu> a écrit :
>Hi Christian,
>
>On Tue, Apr 18, 2017 at 11:07:03PM +0200, Christian Seiler wrote:
>> > 
>> > which is probably due to the fact that I did not changed hmmer2 to
>> > create a shared rather than a static library and lhmmer is not
>compiled
>> > with -fPIC.  What might be the less stressful way to solve this?  I
>> > think the optimal solution would be to craft configure.ac and
>> > Makefile.am for hmmer2 (which only ships configure and Makefile.in)
>and
>> > by doing so create a shared library.  However, I do not consider
>this
>> > as a very fruitful way to spent someones time on orphaned software
>so
>> > a cheaper solution would be welcome.
>> 
>> Well, you could compile the static library with -fPIC anyway. Linking
>> a static library into a shared library is not a problem in and by
>> itself (the code will be copied into the shared library just like it
>> would be copied into an executable), the only problem here is the
>> missing -fPIC.
>> 
>> So if you shoe-horn -fPIC into the compiler flags of the static
>> library, linking that into a dynamic library later should work.
>
>OK, I'll try that.
> 
>> (That said: I'm not a huge fan of this approach, Debian prefers to
>> use shared libraries for a reason. OTOH, if I understand you
>> correctly your second pacakge is the only reverse dependency, so
>> it's not that big of a deal in this case.)
>
>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 ? 

Bastien Ith lintian hat
>
>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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