I found this tip with a Google search & it seems to have fixed this for me
on an Amazon EC2 instance -- it's a bit unbelievable, but the placement of
the -lz flag can matter.
mpicxx -lz code/TheRayGenomeAssembler.a RayPlatform/libRayPlatform.a -o
Ray # fails
mpicxx code/TheRayGenomeAssembler.a RayPlatform/libRayPlatform.a -o Ray -lz
# succeeds
On Fri, May 18, 2012 at 2:15 PM, Sébastien Boisvert <
[email protected]> wrote:
> Someone else is having problem linking the code os Mac OS
>
> Le 2012-05-18 12:57, Egon Ozer a écrit :
>
> I'm running into a little problem compiling 2.0.0-rc7 on OSX 10.6.8. When I
> make with HAVE_LIBZ=y, I get the following error:
>
> mpicxx -lz code/TheRayGenomeAssembler.a RayPlatform/libRayPlatform.a -o Ray
> Undefined symbols:
> "FastqGzLoader::getSize()", referenced from:
> Loader::load(std::basic_string<char, std::char_traits<char>,
> std::allocator<char> >, bool)in TheRayGenomeAssembler.a(Loader.o)
> "FastqGzLoader::open(std::basic_string<char, std::char_traits<char>,
> std::allocator<char> >, int)", referenced from:
> Loader::load(std::basic_string<char, std::char_traits<char>,
> std::allocator<char> >, bool)in TheRayGenomeAssembler.a(Loader.o)
> Loader::load(std::basic_string<char, std::char_traits<char>,
> std::allocator<char> >, bool)in TheRayGenomeAssembler.a(Loader.o)
> "FastqGzLoader::load(int, ArrayOfReads*, MyAllocator*, int)", referenced
> from:
> Loader::loadSequences() in TheRayGenomeAssembler.a(Loader.o)
> ld: symbol(s) not found
> collect2: ld returned 1 exit status
> make: *** [Ray] Error 1
>
> When I run make with HAVE_LIBZ=n, compilation runs without a hitch. I had no
> problems compiling 2.0.0-rc5 with libz.
>
>
>
> This is strange because the build system of Ray has not changed since
> 2.0.0-rc5.
>
>
> Did you change something since 2.0.0-rc5 ?
>
>
>
> Just to make sure, I updated zlib with MacPorts to 1.2.7 (universal), but
> still no dice. Any suggestions?
>
>
> If you have cmake installed, you can build Ray with it instead. CMake is
> cross-platform.
>
>
>
> To build Ray with CMake:
>
>
> tar xjf Ray-v2.0.0-rc7.tar.bz2
>
> cd Ray-v2.0.0-rc7
>
> remove the line " RayPlatform/scheduling/SwitchMan_adapters.cpp" from
> CMakeLists.txt
>
> cd ..
>
> mkdir Build-with-CMAKE
>
> cd Build-with-CMAKE
>
> cmake ../Ray-v2.0.0-rc7
>
> make
>
> ls Ray
>
>
>
> Let me know if that works for you.
>
>
> Thanks,
> - Egon
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