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