On May 22, 2012, at 11:04 AM, Sébastien Boisvert wrote:
> 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.
>
I have GNU Make 3.81. I'll work on updating my 6-years-out-of-date software.
Thanks again.
- E
>
>> 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
>>>> ------------------------------------------------------------------------------
>>>> Live Security Virtual Conference
>>>> Exclusive live event will cover all the ways today's security and
>>>> threat landscape has changed and how IT managers can respond. Discussions
>>>> will include endpoint security, mobile security and the latest in malware
>>>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>>>> _______________________________________________
>>>> Denovoassembler-users mailing list
>>>> [email protected]
>>>> https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
>>>
>>> ------------------------------------------------------------------------------
>>> Live Security Virtual Conference
>>> Exclusive live event will cover all the ways today's security and
>>> threat landscape has changed and how IT managers can respond. Discussions
>>> will include endpoint security, mobile security and the latest in malware
>>> threats.
>>> http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/_______________________________________________
>>> Denovoassembler-users mailing list
>>> [email protected]
>>> https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
>>
>
------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
_______________________________________________
Denovoassembler-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
