[Bioclusters] mpiBlast OS X

[Nick Brockner]

Ok, now that getopt() is out of the way it compiles, but then when it 
goes to link I get this garbage:

ld: Undefined symbols:
std::basic_ostream<char, std::char_traits<char> 
 >::operator<<(std::basic_ostream<char, std::char_traits<char> >& 
(*)(std::basic_ostream<char, std::char_traits<char> >&))
std::basic_ostream<char, std::char_traits<char> >::operator<<(double)
std::basic_ostream<char, std::char_traits<char> >::operator<<(long)
std::basic_ostream<char, std::char_traits<char> >::operator<<(unsigned 
long)
std::basic_string<char, std::char_traits<char>, std::allocator<char> 
 >::_Rep::_M_destroy(std::allocator<char> const&)
.
.
.

I think this has nothing to do with the mpiBlast code, and has 
something to do with Apple's build environment.  Difficult build, this 
is.

Thanks,

-Nick Brockner
On Sep 30, 2004, at 3:35 PM, Aaron Darling wrote:

> This happens on OS X, Solaris, and AIX because our getopt() detection 
> was broken in 1.2.1.  A quick fix is to comment out line 147 of 
> mpiBLAST-1.2.1/src/getopt.h
> e.g. change:
> extern int getopt ();
> to:
> /* extern int getopt (); */
>
> -Aaron
>
> Nick Brockner wrote:
>
>> Hi Aaron,
>>
>> Thanks for the pointer.  Using the Oct. 2003 ncbi toolkit worked for 
>> the previous error, but now I have a more sinister looking error:
>>
>> In file included from /usr/include/pthread.h:61,
>>                  from 
>> /usr/include/gcc/darwin/3.3/c++/ppc-darwin/bits/gthr-default.h:37,
>>                  from 
>> /usr/include/gcc/darwin/3.3/c++/ppc-darwin/bits/gthr.h:98,
>>                  from 
>> /usr/include/gcc/darwin/3.3/c++/ppc-darwin/bits/c++io.h:37,
>>                  from /usr/include/gcc/darwin/3.3/c++/bits/fpos.h:44,
>>                  from /usr/include/gcc/darwin/3.3/c++/iosfwd:49,
>>                  from 
>> /usr/include/gcc/darwin/3.3/c++/bits/stl_algobase.h:70,
>>                  from /usr/include/gcc/darwin/3.3/c++/algorithm:66,
>>                  from mpiblast.cpp:86:
>> /usr/include/unistd.h:183: error: declaration of C function `int 
>> getopt(int,
>>    char* const*, const char*)' conflicts with
>> getopt.h:147: error: previous declaration `int getopt()' here
>> In file included from file_util.hpp:58,
>>                  from mpiblast.hpp:71,
>>                  from mpiblast.cpp:88:
>>
>>
>> Has anyone seen this before? Looks OS X specific.
>>
>> Thanks,
>>
>> -Nick Brockner
>>
>> On Sep 30, 2004, at 2:51 PM, Aaron Darling wrote:
>>
>>> Assuming you are using mpiBLAST 1.2.1, you need to use the October 
>>> 2003 release of the NCBI Toolbox from here:
>>> ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/old/
>>>
>>> Each version of mpiBLAST is designed to compile against a specific 
>>> version of the NCBI Toolbox, as mentioned on our download page here:
>>>
>>> http://mpiblast.lanl.gov/download.html
>>>
>>> Later toolbox releases changed the API to BlastMakeMultQueries and 
>>> BXMLPrintOutput, which is why you are seeing those build errors.
>>>
>>> Regards,
>>> -Aaron
>>>
>>> Nick Brockner wrote:
>>>
>>>> Hi All,
>>>>
>>>> I think I am missing something here, but attempting to compile 
>>>> mpiBlast gets me the following:
>>>>
>>>> blast_hooks.c: In function `getFakeBioseq':
>>>> blast_hooks.c:785: error: too few arguments to function 
>>>> `BlastMakeMultQueries'
>>>> blast_hooks.c: In function `outputResults':
>>>> blast_hooks.c:1334: error: too few arguments to function 
>>>> `BXMLPrintOutput'
>>>> blast_hooks.c:1345: error: too few arguments to function 
>>>> `BXMLPrintOutput'
>>>> blast_hooks.c:1493: error: too few arguments to function 
>>>> `BXMLPrintOutput'
>>>> blast_hooks.c:1498: error: too few arguments to function 
>>>> `BXMLPrintOutput'
>>>> mpicc: No such file or directory
>>>> make[1]: *** [mpiblast-blast_hooks.o] Error 1
>>>> make: *** [all-recursive] Error 1
>>>>
>>>>
>>>> My setup:
>>>> OS X Server 10.3.5
>>>> gcc version 3.3 20030304 (Apple Computer, Inc. build 1495)
>>>> NCBI toolkit installed
>>>> LAM-MPI version 7.0.6
>>>>
>>>>
>>>> Thanks,
>>>>
>>>> -Nick Brockner
>>>>
>>>> _______________________________________________
>>>> Bioclusters maillist  -  Bioclusters@bioinformatics.org
>>>> https://bioinformatics.org/mailman/listinfo/bioclusters
>>>
>>>
>>> _______________________________________________
>>> Bioclusters maillist  -  Bioclusters@bioinformatics.org
>>> https://bioinformatics.org/mailman/listinfo/bioclusters
>>>
>>
>>
>> _______________________________________________
>> Bioclusters maillist  -  Bioclusters@bioinformatics.org
>> https://bioinformatics.org/mailman/listinfo/bioclusters
>
> _______________________________________________
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> https://bioinformatics.org/mailman/listinfo/bioclusters
>
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