Yes, looks like something wrong with the build environment. Looks like it's not linking to the c++ library. Usually the GNU standard c++ library can be linked with -lstdc++. You could either add that to the CXXFLAGS environment variable and reconfigure or just copy the link command, add -lstdc++, and run it from within the src dir. In the past we've only tested releases on Linux and Windows, sounds like that needs to change :) -Aaron Nick Brockner wrote: > 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 >> >> >> _______________________________________________ >> Bioclusters maillist - Bioclusters@bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/bioclusters >> >> > > _______________________________________________ > Bioclusters maillist - Bioclusters@bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bioclusters