[Debian-med-packaging] Bug#756780: [Help] Need help for architecture specific code (Was: Bug#756780: bowtie: FTBFS almost everywhere)

[Andreas Tille]

Hi,

on arm*, powerpc, sparc and  s390x architectures the build problem is:

third_party/cpuid.h: In constructor 'Ebwt<TStr>::Ebwt(int, int32_t, int32_t, int32_t, int32_t, int32_t, const string&, bool, bool, uint32_t, uint32_t, uint32_t, int, std::vector<FileBuf*>&, std::vector<RefRecord>&, std::vector<unsigned int>&, uint32_t, const RefReadInParams&, uint32_t, int32_t, int32_t, bool, bool, bool) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::Alloc<> >; int32_t = int; std::string = std::basic_string<char>; uint32_t = unsigned int]':
third_party/cpuid.h:162:46: error: impossible constraint in 'asm'
   __cpuid (__ext, __eax, __ebx, __ecx, __edx);
                                              ^
third_party/cpuid.h:185:52: error: impossible constraint in 'asm'
   __cpuid (__level, *__eax, *__ebx, *__ecx, *__edx);
                                                    ^
make[2]: *** [bowtie-build] Error 1


on mips* the problem is:


/tmp/cciY8R8w.s:161449: Error: unrecognized opcode `push{l} $14'
/tmp/cciY8R8w.s:161450: Error: unrecognized opcode `popf{l|d}'
/tmp/cciY8R8w.s:161451: Error: unrecognized opcode `pushf{l|d}'
/tmp/cciY8R8w.s:161452: Error: unrecognized opcode `pop{l} $14'
/tmp/cciY8R8w.s:161453: Error: unrecognized opcode `popf{l|d}'
/tmp/cciY8R8w.s:161585: Error: unrecognized opcode `cpuid'
/tmp/cciY8R8w.s:161606: Error: unrecognized opcode `cpuid'
make[2]: *** [bowtie-build] Error 1


and on *-i386 the problem seems to be


  typedef typename Value<TStr>::Type TAlphabet;
                                     ^
ebwt.h: Assembler messages:
ebwt.h:1909: Error: invalid instruction suffix for `popcnt'
ebwt.h:1909: Error: invalid instruction suffix for `popcnt'
ebwt.h:1909: Error: invalid instruction suffix for `popcnt'
ebwt.h:1909: Error: invalid instruction suffix for `popcnt'
make[2]: *** [bowtie-build] Error 1
make[1]: *** [override_dh_auto_build] Error 2
Makefile:211: recipe for target 'bowtie-build' failed


I admit I do not have the slightest idea how to deal with issues
like this.  Any (also partial help) is welcome.

Kind regards

         Andreas.

On Fri, Aug 01, 2014 at 06:20:13PM +0200, Sebastian Ramacher wrote:
> Source: bowtie
> Version: 1.0.1-1
> Severity: serious
> Justification: fails to build from source
> 
> bowtie failed to build on almost every architecture. Please take a look
> at https://buildd.debian.org/status/package.php?p=bowtie
> 
> Cheers
> -- 
> Sebastian Ramacher



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