On Wed, Apr 19, 2017 at 4:20 PM, Andreas Tille <[email protected]> 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 <[email protected]> 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
