[Bioclusters] mpiBlast OS X

[Nick Brockner]

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
>
>
************************************
Nick Brockner
Systems Administrator, Biology Computing Facility
Hamilton College
nbrockne@hamilton.edu
http://www.bio.hamilton.edu/bioinformatics
(315) 859-4137