[Debian-med-packaging] C++ help needed for psortb
Andreas Tille
andreas at an3as.eu
Tue Apr 18 21:01:12 UTC 2017
Hi Walter,
On Tue, Apr 18, 2017 at 01:26:58PM -0700, Walter Landry wrote:
> > hmm-binding.cpp: In member function ‘void HMM::init(char*, int, int)’:
> > hmm-binding.cpp:245:20: error: ‘CUT_NONE’ was not declared in this scope
> > thresh.autocut = CUT_NONE;
> > ^~~~~~~~
> > Makefile:346: recipe for target 'hmm-binding.o' failed
>
> It is difficult to know without spending more time, but I would try
> changing this to
>
> thresh.autocut = threshold_s::CUT_NONE;
Thanks for this quick and helpful hint. :-)
Unfortunately I'm not yet through this issue. A bit later I'm running
into
...
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.
Kind regards
Andreas.
--
http://fam-tille.de
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