Hello,

Le 2012-05-21 10:50, Egon Ozer a écrit :
Thanks to Sébastien and Keith Robinson for the suggestions. I was able to compile with cmake, but still not with libz, for some reason. I also couldn't figure out how to change the order of the tags as suggested by Keith. I was certain I had been able to compile rc5 with libz however (as I have been feeding it gzipped files no problem), so I did a little bit of playing around this morning:

1. I recompiled 2.0-rc5 using "make HAVE_LIBZ=y". Compiled no problem, "./Ray -version" showed "HAVE_LIBZ = y" 2. I recompiled 2.0.0-rc7 using "make HAVE_LIBZ=y". Surprisingly, complied no problem, "./Ray -version" showed "HAVE_LIBZ = y".

As I said, the build system has not changed.

3. Wondering how the heck I got that error message last week, I tried retracing my steps exactly from last week. So I actually modified the Makefile from "HAVE_LIBZ = n" to "HAVE_LIBZ = y", then ran a simple "make" command. Boom. Error recreated.

It looks like, for whatever reason, you have to feed options directly to the make command rather than modifying options in the Makefile. Why? I thought maybe it was the spaces flanking the "=" sign in the Makefile, but when I removed them (i.e. "HAVE_LIBZ=y" instead of "HAVE_LIBZ = y"), the error still recurred.



I guess as long it's working, I don't really care. I just wasn't expecting that modifying the option in the makefile versus feeding it to the make command could make such a difference.


I have not changed the Makefile in a while.

I just tried changing HAVE_LIBZ = y inside the Makefile and it works.

I am using GNU Make 3.82. Maybe you are using a different version or vendor.


Thanks again for the help,


- Egon


On May 18, 2012, at 1:15 PM, Sébastien Boisvert 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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