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

[Christian Seiler]

On 04/18/2017 11:01 PM, Andreas Tille wrote:
> x86_64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/build/psortb-3.0.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro  -shared -L/usr/local/lib -fstack-protector-strong HMM.o hmm-binding.o  -o ../blib/arch/auto/Algorithm/HMM/HMM.so      \
>    -lm -lpthread -lstdc++ -L/usr/local/lib -lhmmer -lsquid      \
> 
> /usr/bin/ld: /usr/lib/gcc/x86_64-linux-gnu/6/../../../x86_64-linux-gnu/libhmmer.a(alphabet.o): relocation R_X86_64_PC32 against symbol `Alphabet' can not be used when making a shared       object; recompile with -fPIC
> /usr/bin/ld: final link failed: Bad value
> collect2: error: ld returned 1 exit status
> ...
> 
> 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.

(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.)

Regards,
Christian