[Bioclusters] mpiblast and mpiformatdb

[Jeremy Mann]

> Hello,
>
> I have uploaded files (in the patches section of
> http://sourceforge.net/projects/mpiblast/)  that implement the following
> changes to mpiformatdb and mpiblast:

I am getting a compiler error when applying these patches:

<snip>

Making all in src
make[1]: Entering directory
`/home/user/jeremy/NCBI/mpiBLAST-1.1.0-patched/src'
source='mpiblast.cpp' object='mpiblast.o' libtool=no \
depfile='.deps/mpiblast.Po' tmpdepfile='.deps/mpiblast.TPo' \
depmode=gcc3 /bin/sh ../depcomp \
mpiCC -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
-DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"mpiBLAST\"
-DVERSION=\"1.1.0\" -DSTDC_HEADERS=1 -D_FILE_OFFSET_BITS=64
-DTIME_WITH_SYS_TIME=1  -I. -I. -I../include/
-I/home/user/jeremy/NCBI/ncbi/include/      -O2
-DINSTALL_PREFIX="\"/usr/local\"" -c -o mpiblast.o `test -f 'mpiblast.cpp'
|| echo './'`mpiblast.cpp
mpiblast.cpp: In member function `void MpiBlast::sendResults(std::string&,
int,
   int)':
mpiblast.cpp:218: `bin' is not a member of type `std::basic_ios<char,
   std::char_traits<char> >'
mpiblast.cpp:248: choosing `std::fpos<_StateT>
   std::fpos<_StateT>::operator-(long int) [with _StateT = mbstate_t]' over `
   operator-'
mpiblast.cpp:248:   because worst conversion for the former is better than
   worst conversion for the latter
make[1]: *** [mpiblast.o] Error 1
make[1]: Leaving directory
`/home/user/jeremy/NCBI/mpiBLAST-1.1.0-patched/src'
make: *** [all-recursive] Error 1

System: Slackware 9.0, Glibc 2.3 and GCC 3.2

-- 
Jeremy Mann
jeremy@biochem.uthscsa.edu

University of Texas Health Science Center
Bioinformatics Core Facility
http://www.bioinformatics.uthscsa.edu
Phone: (210) 567-2672