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

[Andreas Tille]

Hi,

thanks for the hints which I forwarded upstream.  While I've got no
explicit answer about this a new version was released which now even
fails to build on amd64 but with a different error.  My guess is that
this is caused since upstream includes a code copy of an older version
of seqan-dev and we patched the code to cope with the latest version
in Debian.  While beeing no C++ coder I guess another patch for
compatibility with the new version would be needed.

I commited the packaging to SVN[1] and the error message looks like


make[2]: Entering directory '/tmp/buildd/bowtie-1.1.0'
g++ -O3 -DCOMPILER_OPTIONS="\"-O3  -Wl,--hash-style=both -DPOPCNT_CAPABILITY -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -g -O2 -fstack-        protector-strong -Wformat -Werror=format-security  -Wl,-z,relro\""  -Wl,--hash-style=both -DPOPCNT_CAPABILITY -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -Wl,-z,relro  \
        -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -              D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -Wall \
        -I /usr/include/seqan -I third_party -I third_party \
        -o bowtie-build-s ebwt_build.cpp \
        ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp  bowtie_build_main.cpp \
        -lpthread
In file included from blockwise_sa.h:13:0,
                 from ebwt.h:27,
                 from ebwt_build.cpp:11:
diff_sample.h: In member function 'void DifferenceCoverSample<T>::build()':
diff_sample.h:859:3: error: '_Context_LSS' was not declared in this scope
   _Context_LSS<TIndexOff> c;
   ^
diff_sample.h:859:25: error: expected primary-expression before '>' token
   _Context_LSS<TIndexOff> c;
                         ^
diff_sample.h:859:27: error: 'c' was not declared in this scope
   _Context_LSS<TIndexOff> c;
                           ^
Makefile:205: recipe for target 'bowtie-build-s' failed
make[2]: *** [bowtie-build-s] Error 1


Any help would be really welcome

     Andreas.


[1] svn://anonscm.debian.org/debian-med/trunk/packages/bowtie/trunk/




On Mon, Aug 04, 2014 at 12:58:42PM +0100, Wookey wrote:
> +++ Andreas Tille [2014-08-04 09:48 +0200]:
> > 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);
> 
> Those are x86 register names.
> 
> > 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'
> 
> And those are x86 instructions
> 
> So from this info it looks a lot like it is building assembly code
> that can only work on x86.
> 
> You need to either stop this package from building on other
> architectures, or arrange to use C instead of asm on other
> architectures (it may well have some fallback C for this already). 
> This package has probably never been built for anything other than
> amd64 before.  
> 
> This package tries to do some optimised stuff and this code may well
> be about finding out the hardware capabilities in order to optimse
> correctly. You almost certainly don't actually need assembler for that
> and even if it did, intrinsics are usually a much better plan than
> real assembler these days.
> 
> > I admit I do not have the slightest idea how to deal with issues
> > like this.  Any (also partial help) is welcome.
> 
> Hopefully the above will provide some clues. Ask upstream if it's even
> been built for other arches? Look for C fallbacks. Certainly disable
> building x86 ASM on non-x86 arches.
> 
> Wookey
> -- 
> Principal hats:  Linaro, Emdebian, Wookware, Balloonboard, ARM
> http://wookware.org/
> 
> 
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> 

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