[Bioclusters] mpiBlast OS X

[Aaron Darling]

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
>>
>>
> ************************************
> Nick Brockner
> Systems Administrator, Biology Computing Facility
> Hamilton College
> nbrockne@hamilton.edu
> http://www.bio.hamilton.edu/bioinformatics
> (315) 859-4137
>
> _______________________________________________
> Bioclusters maillist  -  Bioclusters@bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bioclusters