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' using GNU General Public License v3 file Makefile.am: Consider adding the COPYING file to the version control system Makefile.am: for your code, to avoid questions about which license your project uses. configure: WARNING: doxygen not found - will not generate any doxygen 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: doxygen not found - will not generate any doxygen 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: doxygen not found - will not generate any doxygen 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/integer/integer_log2.hpp:18, from /tmp/mauve_snapshot/build_scripts/build/include/boost/pending/integer_log2.hpp:7, from /tmp/mauve_snapshot/build_scripts/build/include/boost/pending/lowest_bit.hpp:18, from /tmp/mauve_snapshot/build_scripts/build/include/boost/dynamic_bitset/dynamic_bitset.hpp:45, from /tmp/mauve_snapshot/build_scripts/build/include/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:91:1: 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 /usr/include/aio.h:199: note: expected ‘const struct aiocb * const*’ but argument is of type ‘struct aiocb **’ 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/lib/gcc/x86_64-linux-gnu/4.4.5/../../../../lib/libpthread.a(sem_open.o): In function `sem_open': /home/aurel32/eglibc/eglibc-2.11.3/nptl/sem_open.c:333: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' /usr/lib/gcc/x86_64-linux-gnu/4.4.5/../../../../lib/libpthread.a(sem_open.o): In function `sem_open': /home/aurel32/eglibc/eglibc-2.11.3/nptl/sem_open.c:333: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' /usr/lib/gcc/x86_64-linux-gnu/4.4.5/../../../../lib/libpthread.a(sem_open.o): In function `sem_open': /home/aurel32/eglibc/eglibc-2.11.3/nptl/sem_open.c:333: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' /usr/lib/gcc/x86_64-linux-gnu/4.4.5/../../../../lib/libpthread.a(sem_open.o): In function `sem_open': /home/aurel32/eglibc/eglibc-2.11.3/nptl/sem_open.c:333: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' /usr/lib/gcc/x86_64-linux-gnu/4.4.5/../../../../lib/libpthread.a(sem_open.o): In function `sem_open': /home/aurel32/eglibc/eglibc-2.11.3/nptl/sem_open.c:333: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' /usr/lib/gcc/x86_64-linux-gnu/4.4.5/../../../../lib/libpthread.a(sem_open.o): In function `sem_open': /home/aurel32/eglibc/eglibc-2.11.3/nptl/sem_open.c:333: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' /usr/lib/gcc/x86_64-linux-gnu/4.4.5/../../../../lib/libpthread.a(sem_open.o): In function `sem_open': /home/aurel32/eglibc/eglibc-2.11.3/nptl/sem_open.c:333: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' /usr/lib/gcc/x86_64-linux-gnu/4.4.5/../../../../lib/libpthread.a(sem_open.o): In function `sem_open': /home/aurel32/eglibc/eglibc-2.11.3/nptl/sem_open.c:333: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' /usr/lib/gcc/x86_64-linux-gnu/4.4.5/../../../../lib/libpthread.a(sem_open.o): In function `sem_open': /home/aurel32/eglibc/eglibc-2.11.3/nptl/sem_open.c:333: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' /usr/lib/gcc/x86_64-linux-gnu/4.4.5/../../../../lib/libpthread.a(sem_open.o): In function `sem_open': /home/aurel32/eglibc/eglibc-2.11.3/nptl/sem_open.c:333: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' /usr/lib/gcc/x86_64-linux-gnu/4.4.5/../../../../lib/libpthread.a(sem_open.o): In function `sem_open': /home/aurel32/eglibc/eglibc-2.11.3/nptl/sem_open.c:333: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' /usr/lib/gcc/x86_64-linux-gnu/4.4.5/../../../../lib/libpthread.a(sem_open.o): In function `sem_open': /home/aurel32/eglibc/eglibc-2.11.3/nptl/sem_open.c:333: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' /usr/lib/gcc/x86_64-linux-gnu/4.4.5/../../../../lib/libpthread.a(sem_open.o): In function `sem_open': /home/aurel32/eglibc/eglibc-2.11.3/nptl/sem_open.c:333: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' /usr/lib/gcc/x86_64-linux-gnu/4.4.5/../../../../lib/libpthread.a(sem_open.o): In function `sem_open': /home/aurel32/eglibc/eglibc-2.11.3/nptl/sem_open.c:333: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' /usr/lib/gcc/x86_64-linux-gnu/4.4.5/../../../../lib/libpthread.a(sem_open.o): In function `sem_open': /home/aurel32/eglibc/eglibc-2.11.3/nptl/sem_open.c:333: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' /usr/lib/gcc/x86_64-linux-gnu/4.4.5/../../../../lib/libpthread.a(sem_open.o): In function `sem_open': /home/aurel32/eglibc/eglibc-2.11.3/nptl/sem_open.c:333: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' /usr/lib/gcc/x86_64-linux-gnu/4.4.5/../../../../lib/libpthread.a(sem_open.o): In function `sem_open': /home/aurel32/eglibc/eglibc-2.11.3/nptl/sem_open.c:333: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' /usr/lib/gcc/x86_64-linux-gnu/4.4.5/../../../../lib/libpthread.a(sem_open.o): In function `sem_open': /home/aurel32/eglibc/eglibc-2.11.3/nptl/sem_open.c:333: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' /usr/lib/gcc/x86_64-linux-gnu/4.4.5/../../../../lib/libpthread.a(sem_open.o): In function `sem_open': /home/aurel32/eglibc/eglibc-2.11.3/nptl/sem_open.c:333: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' /usr/lib/gcc/x86_64-linux-gnu/4.4.5/../../../../lib/libpthread.a(sem_open.o): In function `sem_open': /home/aurel32/eglibc/eglibc-2.11.3/nptl/sem_open.c:333: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' /usr/lib/gcc/x86_64-linux-gnu/4.4.5/../../../../lib/libpthread.a(sem_open.o): In function `sem_open': /home/aurel32/eglibc/eglibc-2.11.3/nptl/sem_open.c:333: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' /usr/lib/gcc/x86_64-linux-gnu/4.4.5/../../../../lib/libpthread.a(sem_open.o): In function `sem_open': /home/aurel32/eglibc/eglibc-2.11.3/nptl/sem_open.c:333: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' /usr/lib/gcc/x86_64-linux-gnu/4.4.5/../../../../lib/libpthread.a(sem_open.o): In function `sem_open': /home/aurel32/eglibc/eglibc-2.11.3/nptl/sem_open.c:333: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' /usr/lib/gcc/x86_64-linux-gnu/4.4.5/../../../../lib/libpthread.a(sem_open.o): In function `sem_open': /home/aurel32/eglibc/eglibc-2.11.3/nptl/sem_open.c:333: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' /usr/lib/gcc/x86_64-linux-gnu/4.4.5/../../../../lib/libpthread.a(sem_open.o): In function `sem_open': /home/aurel32/eglibc/eglibc-2.11.3/nptl/sem_open.c:333: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' /usr/lib/gcc/x86_64-linux-gnu/4.4.5/../../../../lib/libpthread.a(sem_open.o): In function `sem_open': /home/aurel32/eglibc/eglibc-2.11.3/nptl/sem_open.c:333: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' /usr/lib/gcc/x86_64-linux-gnu/4.4.5/../../../../lib/libpthread.a(sem_open.o): In function `sem_open': /home/aurel32/eglibc/eglibc-2.11.3/nptl/sem_open.c:333: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' 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' using GNU General Public License v3 file Makefile.am: Consider adding the COPYING file to the version control system Makefile.am: for your code, to avoid questions about which license your project uses. 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 /usr/lib/gcc/x86_64-linux-gnu/4.4.5/../../../../lib/libpthread.a(sem_open.o): In function `sem_open': /home/aurel32/eglibc/eglibc-2.11.3/nptl/sem_open.c:333: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' /usr/lib/gcc/x86_64-linux-gnu/4.4.5/../../../../lib/libpthread.a(sem_open.o): In function `sem_open': /home/aurel32/eglibc/eglibc-2.11.3/nptl/sem_open.c:333: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' /usr/lib/gcc/x86_64-linux-gnu/4.4.5/../../../../lib/libpthread.a(sem_open.o): In function `sem_open': /home/aurel32/eglibc/eglibc-2.11.3/nptl/sem_open.c:333: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' /usr/lib/gcc/x86_64-linux-gnu/4.4.5/../../../../lib/libpthread.a(sem_open.o): In function `sem_open': /home/aurel32/eglibc/eglibc-2.11.3/nptl/sem_open.c:333: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' strip: Warning: 'src' is not an ordinary file strip:src/simujobgen.pl: File format not recognized strip:src/bp_scoring.pl: File format not recognized strip:src/scoregen.pl: File format not recognized strip: Warning: 'src/.deps' is not an ordinary file strip:src/simujobparams.pm: File format not recognized strip:src/rbplocalization.R: File format not recognized strip:src/simujobrun.pl: File format not recognized strip:src/Rgradientgen.pl: File format not recognized 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' repseek/readfst.c: In function ‘readFastaSeq’: repseek/readfst.c:204: warning: passing argument 1 of ‘file2mem’ discards qualifiers from pointer target type repseek/readfst.c:129: note: expected ‘char *’ but argument is of type ‘const char *’ /usr/lib/gcc/x86_64-linux-gnu/4.4.5/../../../../lib/libpthread.a(sem_open.o): In function `sem_open': /home/aurel32/eglibc/eglibc-2.11.3/nptl/sem_open.c:333: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' strip: Warning: 'src' is not an ordinary file strip: Warning: 'src/.deps' 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/.svn' is not an ordinary file strip:src/SeedMatchEnumerator.h: File format not recognized strip: Warning: 'src/tuiuiu' is not an ordinary file