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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