configure.ac:8: installing `config/config.guess'
configure.ac:8: installing `config/config.sub'
configure.ac:61: installing `config/install-sh'
configure.ac:61: installing `config/missing'
libGenome/Makefile.am: installing `config/depcomp'
Makefile.am: installing `./INSTALL'
Makefile.am: installing `./COPYING'
configure: WARNING: latex not found - will not generate doxygen PostScript documentation
configure: WARNING: pdflatex not found - will not generate doxygen PDF documentation
configure.ac:64: installing `config/config.guess'
configure.ac:64: installing `config/config.sub'
configure.ac:52: installing `config/install-sh'
configure.ac:52: installing `config/missing'
libMUSCLE/Makefile.am: installing `config/depcomp'
Makefile.am: installing `./INSTALL'
configure: WARNING: latex not found - will not generate doxygen PostScript documentation
configure: WARNING: pdflatex not found - will not generate doxygen PDF documentation
bittraceback.cpp: In function ‘const char* muscle::BitsToStr(char)’:
bittraceback.cpp:20: warning: deprecated conversion from string constant to ‘char*’
spfast.cpp: In function ‘char* muscle::GapTypeToStr(int)’:
spfast.cpp:20: warning: deprecated conversion from string constant to ‘char*’
spfast.cpp:21: warning: deprecated conversion from string constant to ‘char*’
spfast.cpp:22: warning: deprecated conversion from string constant to ‘char*’
spfast.cpp:23: warning: deprecated conversion from string constant to ‘char*’
spfast.cpp:26: warning: deprecated conversion from string constant to ‘char*’
make[1]: *** No rule to make target `../libMUSCLE/libMUSCLE-3.7.la', needed by `muscle'.  Stop.
make[1]: *** Waiting for unfinished jobs....
make: *** [all-recursive] Error 1
configure.ac:66: installing `config/config.guess'
configure.ac:66: installing `config/config.sub'
configure.ac:54: installing `config/install-sh'
configure.ac:54: installing `config/missing'
libMems/Makefile.am: installing `config/depcomp'
configure: WARNING: latex not found - will not generate doxygen PostScript documentation
configure: WARNING: pdflatex not found - will not generate doxygen PDF documentation
In file included from MuscleInterface.cpp:18:
/tmp/mauve_snapshot/build_scripts/build/include/libMUSCLE-3.7/libMUSCLE/muscle.h:54:1: warning: "assert" redefined
In file included from /tmp/mauve_snapshot/build_scripts/build/include/boost-1_38/boost/pending/integer_log2.hpp:18,
                 from /tmp/mauve_snapshot/build_scripts/build/include/boost-1_38/boost/pending/lowest_bit.hpp:18,
                 from /tmp/mauve_snapshot/build_scripts/build/include/boost-1_38/boost/dynamic_bitset/dynamic_bitset.hpp:41,
                 from /tmp/mauve_snapshot/build_scripts/build/include/boost-1_38/boost/dynamic_bitset.hpp:15,
                 from ../libMems/AbstractMatch.h:21,
                 from ../libMems/SparseAbstractMatch.h:18,
                 from ../libMems/GappedAlignment.h:18,
                 from ../libMems/MuscleInterface.h:19,
                 from MuscleInterface.cpp:13:
/usr/include/assert.h:88:1: warning: this is the location of the previous definition
dmSML/aPOSIXaio.c: In function ‘QueryLastCompletePAIO’:
dmSML/aPOSIXaio.c:115: warning: passing argument 1 of ‘aio_suspend’ from incompatible pointer type
dmSML/util.c: In function ‘removeFile’:
dmSML/util.c:126: warning: assignment discards qualifiers from pointer target type
dmSML/util.c:128: warning: assignment discards qualifiers from pointer target type
configure.ac:9: installing `config/config.guess'
configure.ac:9: installing `config/config.sub'
configure.ac:11: installing `config/install-sh'
configure.ac:11: installing `config/missing'
src/Makefile.am: installing `config/depcomp'
Makefile.am: installing `./INSTALL'
mauveAligner.cpp:47:1: warning: "NELEMS" redefined
In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SlotAllocator.h:20,
                 from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:22,
                 from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h:18,
                 from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Match.h:19,
                 from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchFinder.h:17,
                 from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MemHash.h:20,
                 from mauveAligner.cpp:21:
/tmp/mauve_snapshot/build_scripts/build/include/libMUSCLE-3.7/libMUSCLE/threadstorage.h:22:1: warning: this is the location of the previous definition
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open':
/usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp'
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open':
/usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp'
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open':
/usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp'
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open':
/usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp'
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open':
/usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp'
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open':
/usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp'
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open':
/usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp'
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open':
/usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp'
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open':
/usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp'
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open':
/usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp'
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open':
/usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp'
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open':
/usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp'
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open':
/usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp'
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open':
/usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp'
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open':
/usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp'
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open':
/usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp'
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open':
/usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp'
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open':
/usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp'
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open':
/usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp'
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open':
/usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp'
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open':
/usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp'
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open':
/usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp'
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open':
/usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp'
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open':
/usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp'
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open':
/usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp'
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open':
/usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp'
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open':
/usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp'
strip: Warning: 'src' is not an ordinary file
strip: Warning: 'src/.deps' is not an ordinary file
strip: Warning: 'src/.svn' is not an ordinary file
configure.ac:9: installing `config/config.guess'
configure.ac:9: installing `config/config.sub'
configure.ac:11: installing `config/install-sh'
configure.ac:11: installing `config/missing'
src/Makefile.am: installing `config/depcomp'
Makefile.am: installing `./INSTALL'
Makefile.am: installing `./COPYING'
sgEvolver.cpp:227:1: warning: "NELEMS" redefined
In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SlotAllocator.h:20,
                 from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:22,
                 from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h:18,
                 from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAlignment.h:18,
                 from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h:17,
                 from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:18,
                 from Alignment.h:9,
                 from Mutator.h:13,
                 from sgEvolver.cpp:15:
/tmp/mauve_snapshot/build_scripts/build/include/libMUSCLE-3.7/libMUSCLE/threadstorage.h:22:1: warning: this is the location of the previous definition
cc1: warning: command line option "-Wno-deprecated" is valid for C++/Java/ObjC++ but not for C
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open':
/usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp'
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open':
/usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp'
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open':
/usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp'
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open':
/usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp'
strip: Warning: 'src' is not an ordinary file
strip:src/simujobgen.pl: File format not recognized
strip:src/rbplocalization.R: File format not recognized
strip: Warning: 'src/.deps' is not an ordinary file
strip:src/scoregen.pl: File format not recognized
strip:src/bp_scoring.pl: File format not recognized
strip: Warning: 'src/.svn' is not an ordinary file
strip:src/simujobrun.pl: File format not recognized
strip:src/Rgradientgen.pl: File format not recognized
strip:src/simujobparams.pm: File format not recognized
configure.ac:9: installing `config/config.guess'
configure.ac:9: installing `config/config.sub'
configure.ac:11: installing `config/install-sh'
configure.ac:11: installing `config/missing'
src/Makefile.am: installing `config/depcomp'
Makefile.am: installing `./INSTALL'
cc1: warning: command line option "-Wno-deprecated" is valid for C++/Java/ObjC++ but not for C
cc1: warning: command line option "-Wno-deprecated" is valid for C++/Java/ObjC++ but not for C
cc1: warning: command line option "-Wno-deprecated" is valid for C++/Java/ObjC++ but not for C
cc1: warning: command line option "-Wno-deprecated" is valid for C++/Java/ObjC++ but not for C
cc1: warning: command line option "-Wno-deprecated" is valid for C++/Java/ObjC++ but not for C
cc1: warning: command line option "-Wno-deprecated" is valid for C++/Java/ObjC++ but not for C
cc1: warning: command line option "-Wno-deprecated" is valid for C++/Java/ObjC++ but not for C
cc1: warning: command line option "-Wno-deprecated" is valid for C++/Java/ObjC++ but not for C
cc1: warning: command line option "-Wno-deprecated" is valid for C++/Java/ObjC++ but not for C
cc1: warning: command line option "-Wno-deprecated" is valid for C++/Java/ObjC++ but not for C
cc1: warning: command line option "-Wno-deprecated" is valid for C++/Java/ObjC++ but not for C
cc1: warning: command line option "-Wno-deprecated" is valid for C++/Java/ObjC++ but not for C
cc1: warning: command line option "-Wno-deprecated" is valid for C++/Java/ObjC++ but not for C
cc1: warning: command line option "-Wno-deprecated" is valid for C++/Java/ObjC++ but not for C
cc1: warning: command line option "-Wno-deprecated" is valid for C++/Java/ObjC++ but not for C
cc1: warning: command line option "-Wno-deprecated" is valid for C++/Java/ObjC++ but not for C
cc1: warning: command line option "-Wno-deprecated" is valid for C++/Java/ObjC++ but not for C
cc1: warning: command line option "-Wno-deprecated" is valid for C++/Java/ObjC++ but not for C
cc1: warning: command line option "-Wno-deprecated" is valid for C++/Java/ObjC++ but not for C
cc1: warning: command line option "-Wno-deprecated" is valid for C++/Java/ObjC++ but not for C
cc1: warning: command line option "-Wno-deprecated" is valid for C++/Java/ObjC++ but not for C
cc1: warning: command line option "-Wno-deprecated" is valid for C++/Java/ObjC++ but not for C
cc1: warning: command line option "-Wno-deprecated" is valid for C++/Java/ObjC++ but not for C
cc1: warning: command line option "-Wno-deprecated" is valid for C++/Java/ObjC++ but not for C
cc1: warning: command line option "-Wno-deprecated" is valid for C++/Java/ObjC++ but not for C
cc1: warning: command line option "-Wno-deprecated" is valid for C++/Java/ObjC++ but not for C
repseek/readfst.c: In function ‘readFastaSeq’:
repseek/readfst.c:204: warning: passing argument 1 of ‘file2mem’ discards qualifiers from pointer target type
cc1: warning: command line option "-Wno-deprecated" is valid for C++/Java/ObjC++ but not for C
cc1: warning: command line option "-Wno-deprecated" is valid for C++/Java/ObjC++ but not for C
cc1: warning: command line option "-Wno-deprecated" is valid for C++/Java/ObjC++ but not for C
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open':
/usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp'
strip: Warning: 'src' is not an ordinary file
strip: Warning: 'src/repseek' is not an ordinary file
strip:src/MatchRecord.h: File format not recognized
strip: Warning: 'src/tuiuiu' is not an ordinary file
strip:src/SeedMatchEnumerator.h: File format not recognized
strip: Warning: 'src/.deps' is not an ordinary file
strip: Warning: 'src/.svn' is not an ordinary file