Mock Version: 0.9.14 Mock Version: 0.9.14 ENTER do(['bash', '--login', '-c', 'rpmbuild -bs --target x86_64 --nodeps builddir/build/SPECS/ghmm.spec'], False, '/var/lib/mock/dist-f13-build-632355-91420/root/', None, 86400, True, 0, 427, 102, None, logger=) Executing command: ['bash', '--login', '-c', 'rpmbuild -bs --target x86_64 --nodeps builddir/build/SPECS/ghmm.spec'] sh: /usr/bin/python: No such file or directory sh: /usr/bin/python: No such file or directory sh: /usr/bin/python: No such file or directory sh: /usr/bin/python: No such file or directory warning: Could not canonicalize hostname: x86-1.fedora.phx.redhat.com Building target platforms: x86_64 Building for target x86_64 Wrote: /builddir/build/SRPMS/ghmm-0.7-4.svn2286.fc13.src.rpm Child returncode was: 0 LEAVE do --> ENTER do(['bash', '--login', '-c', 'rpmbuild -bb --target x86_64 --nodeps builddir/build/SPECS/ghmm.spec'], False, '/var/lib/mock/dist-f13-build-632355-91420/root/', None, 86400, True, 0, 427, 102, None, logger=) Executing command: ['bash', '--login', '-c', 'rpmbuild -bb --target x86_64 --nodeps builddir/build/SPECS/ghmm.spec'] Building target platforms: x86_64 Building for target x86_64 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.LyPHxV + umask 022 + cd /builddir/build/BUILD + LANG=C + export LANG + unset DISPLAY + cd /builddir/build/BUILD + rm -rf ghmm + /usr/bin/bzip2 -dc /builddir/build/SOURCES/ghmm.tar.bz2 + /bin/tar -xf - + STATUS=0 + '[' 0 -ne 0 ']' + cd ghmm + /bin/chmod -Rf a+rX,u+w,g-w,o-w . + sed -i -e 's|$(PYTHON) setup.py install.*$|$(PYTHON) setup.py install -O1 --skip-build --root ${RPM_BUILD_ROOT}|' ghmmwrapper/Makefile.am HMMEd/Makefile.am + sed -i -e 1,1d ghmmwrapper/ghmm_gato/xmlutil.py ghmmwrapper/ghmm_gato/HMMEd.py ghmmwrapper/ghmm_gato/EditObjectAttributesDialog.py ghmmwrapper/ghmm.py HMMEd/HMMEditor.py HMMEd/ObjectHMM.py HMMEd/HMMEditingContext.py + find . -type f -name '*.c' + xargs chmod -x + find . -type f -name '*.h' + xargs chmod -x + find . -type f -name '*.txt' + xargs chmod -x + chmod 644 AUTHORS + for i in AUTHORS + iconv -f iso8859-1 -t utf-8 AUTHORS + touch -r AUTHORS AUTHORS.new + mv AUTHORS.new AUTHORS + echo 'Patch #0 (ghmm-make-check.patch):' Patch #0 (ghmm-make-check.patch): + /bin/cat /builddir/build/SOURCES/ghmm-make-check.patch + /usr/bin/patch -s -p0 --fuzz=0 + echo 'Patch #1 (ghmm-config.patch):' Patch #1 (ghmm-config.patch): + /bin/cat /builddir/build/SOURCES/ghmm-config.patch + /usr/bin/patch -s -p0 --fuzz=0 + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.sbP7eh + umask 022 + cd /builddir/build/BUILD + cd ghmm + LANG=C + export LANG + unset DISPLAY + ./autogen.sh configure.in:30: installing `./config.guess' configure.in:30: installing `./config.sub' configure.in:16: installing `./install-sh' configure.in:16: installing `./missing' ghmm/Makefile.am: installing `./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. + export 'CFLAGS= -I/usr/include/atlas' + CFLAGS=' -I/usr/include/atlas' + CFLAGS=' -I/usr/include/atlas' + export CFLAGS + CXXFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic' + export CXXFLAGS + FFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -I/usr/lib64/gfortran/modules' + export FFLAGS + ./configure --build=x86_64-redhat-linux-gnu --host=x86_64-redhat-linux-gnu --target=x86_64-redhat-linux-gnu --program-prefix= --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info --enable-gsl --enable-experimental --enable-unsupported --enable-atlas configure: WARNING: unrecognized options: --enable-experimental checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking for x86_64-redhat-linux-gnu-gcc... no checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of gcc... gcc3 checking build system type... x86_64-redhat-linux-gnu checking host system type... x86_64-redhat-linux-gnu checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 98304 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking for /usr/bin/ld option to reload object files... -r checking for x86_64-redhat-linux-gnu-objdump... no checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for x86_64-redhat-linux-gnu-ar... no checking for ar... ar checking for x86_64-redhat-linux-gnu-strip... no checking for strip... strip checking for x86_64-redhat-linux-gnu-ranlib... no checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... no checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for gawk... (cached) gawk checking for doxygen... no checking for rm... /bin/rm checking for pkg-config... /usr/bin/pkg-config checking for expect... no checking for runtest... no configure: obsolete features enabled configure: unsupported features enabled checking for pthread_join in -lpthread... yes checking for ANSI C header files... (cached) yes checking for an ANSI C-conforming const... yes checking for size_t... yes checking whether time.h and sys/time.h may both be included... yes checking whether struct tm is in sys/time.h or time.h... time.h checking for sqrt in -lm... yes checking for exp in -lm... yes checking for pow in -lm... yes checking for gsl-config... /usr/bin/gsl-config checking for GSL - version >= 0.7... yes checking for gsl_inteval... no checking whether gsl_root_fsolver_alloc takes one argument... yes checking for gsl_histogram_set_ranges_uniform... yes configure: using GSL random number generator checking for lapack with pkg-config... no configure: lapack not found with pkg-config configure: you have to add the necessary flags to CFLAGS checking for clapack_dgetrf in -llapack... yes checking for clapack_dgetri in -llapack... yes checking for clapack_dpotrf in -llapack... yes checking libxml2 version... ... ok checking for python... /usr/bin/python configure: creating ./config.status config.status: creating Makefile config.status: creating ghmm/Makefile config.status: creating ghmm/ghmmconfig.h config.status: creating tools/Makefile config.status: creating tests/Makefile config.status: creating tests/data/Makefile config.status: creating tools/ghmm-config config.status: creating ghmmwrapper/Makefile config.status: creating HMMEd/Makefile config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands /bin/rm: cannot remove `libtoolT': No such file or directory configure: WARNING: unrecognized options: --enable-experimental + make -j4 make all-recursive make[1]: Entering directory `/builddir/build/BUILD/ghmm' Making all in ghmm make[2]: Entering directory `/builddir/build/BUILD/ghmm/ghmm' Making all in . make[3]: Entering directory `/builddir/build/BUILD/ghmm/ghmm' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT rng.lo -MD -MP -MF .deps/rng.Tpo -c -o rng.lo rng.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT randvar.lo -MD -MP -MF .deps/randvar.Tpo -c -o randvar.lo randvar.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT matrixop.lo -MD -MP -MF .deps/matrixop.Tpo -c -o matrixop.lo matrixop.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT gauss_tail.lo -MD -MP -MF .deps/gauss_tail.Tpo -c -o gauss_tail.lo gauss_tail.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT randvar.lo -MD -MP -MF .deps/randvar.Tpo -c randvar.c -fPIC -DPIC -o .libs/randvar.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT matrixop.lo -MD -MP -MF .deps/matrixop.Tpo -c matrixop.c -fPIC -DPIC -o .libs/matrixop.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT gauss_tail.lo -MD -MP -MF .deps/gauss_tail.Tpo -c gauss_tail.c -fPIC -DPIC -o .libs/gauss_tail.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT rng.lo -MD -MP -MF .deps/rng.Tpo -c rng.c -fPIC -DPIC -o .libs/rng.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT rng.lo -MD -MP -MF .deps/rng.Tpo -c rng.c -o rng.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT gauss_tail.lo -MD -MP -MF .deps/gauss_tail.Tpo -c gauss_tail.c -o gauss_tail.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT matrixop.lo -MD -MP -MF .deps/matrixop.Tpo -c matrixop.c -o matrixop.o >/dev/null 2>&1 mv -f .deps/rng.Tpo .deps/rng.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT mes.lo -MD -MP -MF .deps/mes.Tpo -c -o mes.lo mes.c mv -f .deps/gauss_tail.Tpo .deps/gauss_tail.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT ghmm_internals.lo -MD -MP -MF .deps/ghmm_internals.Tpo -c -o ghmm_internals.lo ghmm_internals.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT mes.lo -MD -MP -MF .deps/mes.Tpo -c mes.c -fPIC -DPIC -o .libs/mes.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT randvar.lo -MD -MP -MF .deps/randvar.Tpo -c randvar.c -o randvar.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT ghmm_internals.lo -MD -MP -MF .deps/ghmm_internals.Tpo -c ghmm_internals.c -fPIC -DPIC -o .libs/ghmm_internals.o mv -f .deps/matrixop.Tpo .deps/matrixop.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT mprintf.lo -MD -MP -MF .deps/mprintf.Tpo -c -o mprintf.lo mprintf.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT ghmm_internals.lo -MD -MP -MF .deps/ghmm_internals.Tpo -c ghmm_internals.c -o ghmm_internals.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT mprintf.lo -MD -MP -MF .deps/mprintf.Tpo -c mprintf.c -fPIC -DPIC -o .libs/mprintf.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT mes.lo -MD -MP -MF .deps/mes.Tpo -c mes.c -o mes.o >/dev/null 2>&1 mv -f .deps/ghmm_internals.Tpo .deps/ghmm_internals.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT vector.lo -MD -MP -MF .deps/vector.Tpo -c -o vector.lo vector.c mv -f .deps/randvar.Tpo .deps/randvar.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT matrix.lo -MD -MP -MF .deps/matrix.Tpo -c -o matrix.lo matrix.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT vector.lo -MD -MP -MF .deps/vector.Tpo -c vector.c -fPIC -DPIC -o .libs/vector.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT mprintf.lo -MD -MP -MF .deps/mprintf.Tpo -c mprintf.c -o mprintf.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT matrix.lo -MD -MP -MF .deps/matrix.Tpo -c matrix.c -fPIC -DPIC -o .libs/matrix.o mv -f .deps/mes.Tpo .deps/mes.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT scanner.lo -MD -MP -MF .deps/scanner.Tpo -c -o scanner.lo scanner.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT vector.lo -MD -MP -MF .deps/vector.Tpo -c vector.c -o vector.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT scanner.lo -MD -MP -MF .deps/scanner.Tpo -c scanner.c -fPIC -DPIC -o .libs/scanner.o mv -f .deps/mprintf.Tpo .deps/mprintf.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT linkedlist.lo -MD -MP -MF .deps/linkedlist.Tpo -c -o linkedlist.lo linkedlist.c mv -f .deps/vector.Tpo .deps/vector.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT sequence.lo -MD -MP -MF .deps/sequence.Tpo -c -o sequence.lo sequence.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT linkedlist.lo -MD -MP -MF .deps/linkedlist.Tpo -c linkedlist.c -fPIC -DPIC -o .libs/linkedlist.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT matrix.lo -MD -MP -MF .deps/matrix.Tpo -c matrix.c -o matrix.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT sequence.lo -MD -MP -MF .deps/sequence.Tpo -c sequence.c -fPIC -DPIC -o .libs/sequence.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT linkedlist.lo -MD -MP -MF .deps/linkedlist.Tpo -c linkedlist.c -o linkedlist.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT scanner.lo -MD -MP -MF .deps/scanner.Tpo -c scanner.c -o scanner.o >/dev/null 2>&1 mv -f .deps/linkedlist.Tpo .deps/linkedlist.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT psequence.lo -MD -MP -MF .deps/psequence.Tpo -c -o psequence.lo psequence.c mv -f .deps/matrix.Tpo .deps/matrix.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT xmlreader.lo -MD -MP -MF .deps/xmlreader.Tpo -c -o xmlreader.lo xmlreader.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT psequence.lo -MD -MP -MF .deps/psequence.Tpo -c psequence.c -fPIC -DPIC -o .libs/psequence.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT xmlreader.lo -MD -MP -MF .deps/xmlreader.Tpo -c xmlreader.c -fPIC -DPIC -o .libs/xmlreader.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT psequence.lo -MD -MP -MF .deps/psequence.Tpo -c psequence.c -o psequence.o >/dev/null 2>&1 mv -f .deps/scanner.Tpo .deps/scanner.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT xmlwriter.lo -MD -MP -MF .deps/xmlwriter.Tpo -c -o xmlwriter.lo xmlwriter.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT xmlwriter.lo -MD -MP -MF .deps/xmlwriter.Tpo -c xmlwriter.c -fPIC -DPIC -o .libs/xmlwriter.o mv -f .deps/psequence.Tpo .deps/psequence.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT model.lo -MD -MP -MF .deps/model.Tpo -c -o model.lo model.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT model.lo -MD -MP -MF .deps/model.Tpo -c model.c -fPIC -DPIC -o .libs/model.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT sequence.lo -MD -MP -MF .deps/sequence.Tpo -c sequence.c -o sequence.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT xmlreader.lo -MD -MP -MF .deps/xmlreader.Tpo -c xmlreader.c -o xmlreader.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT xmlwriter.lo -MD -MP -MF .deps/xmlwriter.Tpo -c xmlwriter.c -o xmlwriter.o >/dev/null 2>&1 mv -f .deps/sequence.Tpo .deps/sequence.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT foba.lo -MD -MP -MF .deps/foba.Tpo -c -o foba.lo foba.c mv -f .deps/xmlwriter.Tpo .deps/xmlwriter.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT viterbi.lo -MD -MP -MF .deps/viterbi.Tpo -c -o viterbi.lo viterbi.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT foba.lo -MD -MP -MF .deps/foba.Tpo -c foba.c -fPIC -DPIC -o .libs/foba.o mv -f .deps/xmlreader.Tpo .deps/xmlreader.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT reestimate.lo -MD -MP -MF .deps/reestimate.Tpo -c -o reestimate.lo reestimate.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT viterbi.lo -MD -MP -MF .deps/viterbi.Tpo -c viterbi.c -fPIC -DPIC -o .libs/viterbi.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT reestimate.lo -MD -MP -MF .deps/reestimate.Tpo -c reestimate.c -fPIC -DPIC -o .libs/reestimate.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT model.lo -MD -MP -MF .deps/model.Tpo -c model.c -o model.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT viterbi.lo -MD -MP -MF .deps/viterbi.Tpo -c viterbi.c -o viterbi.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT foba.lo -MD -MP -MF .deps/foba.Tpo -c foba.c -o foba.o >/dev/null 2>&1 mv -f .deps/viterbi.Tpo .deps/viterbi.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT gradescent.lo -MD -MP -MF .deps/gradescent.Tpo -c -o gradescent.lo gradescent.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT gradescent.lo -MD -MP -MF .deps/gradescent.Tpo -c gradescent.c -fPIC -DPIC -o .libs/gradescent.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT reestimate.lo -MD -MP -MF .deps/reestimate.Tpo -c reestimate.c -o reestimate.o >/dev/null 2>&1 mv -f .deps/foba.Tpo .deps/foba.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT gradescent.lo -MD -MP -MF .deps/gradescent.Tpo -c gradescent.c -o gradescent.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT kbest.lo -MD -MP -MF .deps/kbest.Tpo -c -o kbest.lo kbest.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT kbest.lo -MD -MP -MF .deps/kbest.Tpo -c kbest.c -fPIC -DPIC -o .libs/kbest.o mv -f .deps/gradescent.Tpo .deps/gradescent.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT discrime.lo -MD -MP -MF .deps/discrime.Tpo -c -o discrime.lo discrime.c mv -f .deps/reestimate.Tpo .deps/reestimate.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT modelutil.lo -MD -MP -MF .deps/modelutil.Tpo -c -o modelutil.lo modelutil.c mv -f .deps/model.Tpo .deps/model.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT cluster.lo -MD -MP -MF .deps/cluster.Tpo -c -o cluster.lo cluster.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT discrime.lo -MD -MP -MF .deps/discrime.Tpo -c discrime.c -fPIC -DPIC -o .libs/discrime.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT kbest.lo -MD -MP -MF .deps/kbest.Tpo -c kbest.c -o kbest.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT cluster.lo -MD -MP -MF .deps/cluster.Tpo -c cluster.c -fPIC -DPIC -o .libs/cluster.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT modelutil.lo -MD -MP -MF .deps/modelutil.Tpo -c modelutil.c -fPIC -DPIC -o .libs/modelutil.o cluster.c: In function 'ghmm_cluster_hmm': cluster.c:94: warning: passing argument 1 of 'ghmm_dseq_print' from incompatible pointer type sequence.h:268: note: expected 'struct ghmm_dseq *' but argument is of type 'struct FILE *' cluster.c:94: warning: passing argument 2 of 'ghmm_dseq_print' from incompatible pointer type sequence.h:268: note: expected 'struct FILE *' but argument is of type 'struct ghmm_dseq *' libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT modelutil.lo -MD -MP -MF .deps/modelutil.Tpo -c modelutil.c -o modelutil.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT cluster.lo -MD -MP -MF .deps/cluster.Tpo -c cluster.c -o cluster.o >/dev/null 2>&1 mv -f .deps/kbest.Tpo .deps/kbest.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT root_finder.lo -MD -MP -MF .deps/root_finder.Tpo -c -o root_finder.lo root_finder.c mv -f .deps/modelutil.Tpo .deps/modelutil.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT smodel.lo -MD -MP -MF .deps/smodel.Tpo -c -o smodel.lo smodel.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT root_finder.lo -MD -MP -MF .deps/root_finder.Tpo -c root_finder.c -fPIC -DPIC -o .libs/root_finder.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT smodel.lo -MD -MP -MF .deps/smodel.Tpo -c smodel.c -fPIC -DPIC -o .libs/smodel.o mv -f .deps/cluster.Tpo .deps/cluster.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT sfoba.lo -MD -MP -MF .deps/sfoba.Tpo -c -o sfoba.lo sfoba.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT sfoba.lo -MD -MP -MF .deps/sfoba.Tpo -c sfoba.c -fPIC -DPIC -o .libs/sfoba.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT root_finder.lo -MD -MP -MF .deps/root_finder.Tpo -c root_finder.c -o root_finder.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT discrime.lo -MD -MP -MF .deps/discrime.Tpo -c discrime.c -o discrime.o >/dev/null 2>&1 mv -f .deps/root_finder.Tpo .deps/root_finder.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT sviterbi.lo -MD -MP -MF .deps/sviterbi.Tpo -c -o sviterbi.lo sviterbi.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT sviterbi.lo -MD -MP -MF .deps/sviterbi.Tpo -c sviterbi.c -fPIC -DPIC -o .libs/sviterbi.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT sfoba.lo -MD -MP -MF .deps/sfoba.Tpo -c sfoba.c -o sfoba.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT sviterbi.lo -MD -MP -MF .deps/sviterbi.Tpo -c sviterbi.c -o sviterbi.o >/dev/null 2>&1 mv -f .deps/sfoba.Tpo .deps/sfoba.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT sreestimate.lo -MD -MP -MF .deps/sreestimate.Tpo -c -o sreestimate.lo sreestimate.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT sreestimate.lo -MD -MP -MF .deps/sreestimate.Tpo -c sreestimate.c -fPIC -DPIC -o .libs/sreestimate.o mv -f .deps/sviterbi.Tpo .deps/sviterbi.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT scluster.lo -MD -MP -MF .deps/scluster.Tpo -c -o scluster.lo scluster.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT smodel.lo -MD -MP -MF .deps/smodel.Tpo -c smodel.c -o smodel.o >/dev/null 2>&1 mv -f .deps/discrime.Tpo .deps/discrime.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT sgenerate.lo -MD -MP -MF .deps/sgenerate.Tpo -c -o sgenerate.lo sgenerate.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT scluster.lo -MD -MP -MF .deps/scluster.Tpo -c scluster.c -fPIC -DPIC -o .libs/scluster.o scluster.c: In function 'ghmm_scluster_hmm': scluster.c:366: warning: passing argument 1 of 'ghmm_cseq_print' from incompatible pointer type sequence.h:293: note: expected 'struct ghmm_cseq *' but argument is of type 'struct _IO_FILE *' scluster.c:366: warning: passing argument 2 of 'ghmm_cseq_print' from incompatible pointer type sequence.h:293: note: expected 'struct FILE *' but argument is of type 'struct ghmm_cseq *' scluster.c: In function 'ghmm_scluster_out': scluster.c:563: warning: passing argument 1 of 'ghmm_cseq_print' from incompatible pointer type sequence.h:293: note: expected 'struct ghmm_cseq *' but argument is of type 'struct FILE *' scluster.c:563: warning: passing argument 2 of 'ghmm_cseq_print' from incompatible pointer type sequence.h:293: note: expected 'struct FILE *' but argument is of type 'struct ghmm_cseq *' libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT sgenerate.lo -MD -MP -MF .deps/sgenerate.Tpo -c sgenerate.c -fPIC -DPIC -o .libs/sgenerate.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT sreestimate.lo -MD -MP -MF .deps/sreestimate.Tpo -c sreestimate.c -o sreestimate.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT scluster.lo -MD -MP -MF .deps/scluster.Tpo -c scluster.c -o scluster.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT sgenerate.lo -MD -MP -MF .deps/sgenerate.Tpo -c sgenerate.c -o sgenerate.o >/dev/null 2>&1 mv -f .deps/scluster.Tpo .deps/scluster.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT smixturehmm.lo -MD -MP -MF .deps/smixturehmm.Tpo -c -o smixturehmm.lo smixturehmm.c mv -f .deps/sgenerate.Tpo .deps/sgenerate.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT smap_classify.lo -MD -MP -MF .deps/smap_classify.Tpo -c -o smap_classify.lo smap_classify.c mv -f .deps/sreestimate.Tpo .deps/sreestimate.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT sdmodel.lo -MD -MP -MF .deps/sdmodel.Tpo -c -o sdmodel.lo sdmodel.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT smap_classify.lo -MD -MP -MF .deps/smap_classify.Tpo -c smap_classify.c -fPIC -DPIC -o .libs/smap_classify.o mv -f .deps/smodel.Tpo .deps/smodel.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT smixturehmm.lo -MD -MP -MF .deps/smixturehmm.Tpo -c smixturehmm.c -fPIC -DPIC -o .libs/smixturehmm.o /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT sdfoba.lo -MD -MP -MF .deps/sdfoba.Tpo -c -o sdfoba.lo sdfoba.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT sdmodel.lo -MD -MP -MF .deps/sdmodel.Tpo -c sdmodel.c -fPIC -DPIC -o .libs/sdmodel.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT sdfoba.lo -MD -MP -MF .deps/sdfoba.Tpo -c sdfoba.c -fPIC -DPIC -o .libs/sdfoba.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT smixturehmm.lo -MD -MP -MF .deps/smixturehmm.Tpo -c smixturehmm.c -o smixturehmm.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT smap_classify.lo -MD -MP -MF .deps/smap_classify.Tpo -c smap_classify.c -o smap_classify.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT sdfoba.lo -MD -MP -MF .deps/sdfoba.Tpo -c sdfoba.c -o sdfoba.o >/dev/null 2>&1 mv -f .deps/smixturehmm.Tpo .deps/smixturehmm.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT sdviterbi.lo -MD -MP -MF .deps/sdviterbi.Tpo -c -o sdviterbi.lo sdviterbi.c mv -f .deps/smap_classify.Tpo .deps/smap_classify.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT pmodel.lo -MD -MP -MF .deps/pmodel.Tpo -c -o pmodel.lo pmodel.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT sdmodel.lo -MD -MP -MF .deps/sdmodel.Tpo -c sdmodel.c -o sdmodel.o >/dev/null 2>&1 mv -f .deps/sdfoba.Tpo .deps/sdfoba.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT pviterbi.lo -MD -MP -MF .deps/pviterbi.Tpo -c -o pviterbi.lo pviterbi.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT pviterbi.lo -MD -MP -MF .deps/pviterbi.Tpo -c pviterbi.c -fPIC -DPIC -o .libs/pviterbi.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT sdviterbi.lo -MD -MP -MF .deps/sdviterbi.Tpo -c sdviterbi.c -fPIC -DPIC -o .libs/sdviterbi.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT pmodel.lo -MD -MP -MF .deps/pmodel.Tpo -c pmodel.c -fPIC -DPIC -o .libs/pmodel.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT pmodel.lo -MD -MP -MF .deps/pmodel.Tpo -c pmodel.c -o pmodel.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT sdviterbi.lo -MD -MP -MF .deps/sdviterbi.Tpo -c sdviterbi.c -o sdviterbi.o >/dev/null 2>&1 mv -f .deps/sdmodel.Tpo .deps/sdmodel.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT pviterbi_propagate.lo -MD -MP -MF .deps/pviterbi_propagate.Tpo -c -o pviterbi_propagate.lo pviterbi_propagate.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT pviterbi.lo -MD -MP -MF .deps/pviterbi.Tpo -c pviterbi.c -o pviterbi.o >/dev/null 2>&1 mv -f .deps/pmodel.Tpo .deps/pmodel.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT pviterbi_propagate.lo -MD -MP -MF .deps/pviterbi_propagate.Tpo -c pviterbi_propagate.c -fPIC -DPIC -o .libs/pviterbi_propagate.o mv -f .deps/sdviterbi.Tpo .deps/sdviterbi.Plo mv -f .deps/pviterbi.Tpo .deps/pviterbi.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT pviterbi_propagate.lo -MD -MP -MF .deps/pviterbi_propagate.Tpo -c pviterbi_propagate.c -o pviterbi_propagate.o >/dev/null 2>&1 mv -f .deps/pviterbi_propagate.Tpo .deps/pviterbi_propagate.Plo /bin/sh ../libtool --tag=CC --mode=link gcc -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -version-info 1:0:0 -o libghmm.la -rpath /usr/lib64 rng.lo randvar.lo matrixop.lo gauss_tail.lo mes.lo ghmm_internals.lo mprintf.lo vector.lo matrix.lo scanner.lo linkedlist.lo sequence.lo psequence.lo xmlreader.lo xmlwriter.lo model.lo foba.lo viterbi.lo reestimate.lo gradescent.lo kbest.lo discrime.lo modelutil.lo cluster.lo root_finder.lo smodel.lo sfoba.lo sviterbi.lo sreestimate.lo scluster.lo sgenerate.lo smixturehmm.lo smap_classify.lo sdmodel.lo sdfoba.lo sdviterbi.lo pmodel.lo pviterbi.lo pviterbi_propagate.lo -lm -lm -lm -lpthread -lgsl -lgslcblas -lm -lxml2 libtool: link: gcc -shared .libs/rng.o .libs/randvar.o .libs/matrixop.o .libs/gauss_tail.o .libs/mes.o .libs/ghmm_internals.o .libs/mprintf.o .libs/vector.o .libs/matrix.o .libs/scanner.o .libs/linkedlist.o .libs/sequence.o .libs/psequence.o .libs/xmlreader.o .libs/xmlwriter.o .libs/model.o .libs/foba.o .libs/viterbi.o .libs/reestimate.o .libs/gradescent.o .libs/kbest.o .libs/discrime.o .libs/modelutil.o .libs/cluster.o .libs/root_finder.o .libs/smodel.o .libs/sfoba.o .libs/sviterbi.o .libs/sreestimate.o .libs/scluster.o .libs/sgenerate.o .libs/smixturehmm.o .libs/smap_classify.o .libs/sdmodel.o .libs/sdfoba.o .libs/sdviterbi.o .libs/pmodel.o .libs/pviterbi.o .libs/pviterbi_propagate.o -lpthread -lgsl -lgslcblas -lm -lxml2 -Wl,-soname -Wl,libghmm.so.1 -o .libs/libghmm.so.1.0.0 libtool: link: (cd ".libs" && rm -f "libghmm.so.1" && ln -s "libghmm.so.1.0.0" "libghmm.so.1") libtool: link: (cd ".libs" && rm -f "libghmm.so" && ln -s "libghmm.so.1.0.0" "libghmm.so") libtool: link: ar cru .libs/libghmm.a rng.o randvar.o matrixop.o gauss_tail.o mes.o ghmm_internals.o mprintf.o vector.o matrix.o scanner.o linkedlist.o sequence.o psequence.o xmlreader.o xmlwriter.o model.o foba.o viterbi.o reestimate.o gradescent.o kbest.o discrime.o modelutil.o cluster.o root_finder.o smodel.o sfoba.o sviterbi.o sreestimate.o scluster.o sgenerate.o smixturehmm.o smap_classify.o sdmodel.o sdfoba.o sdviterbi.o pmodel.o pviterbi.o pviterbi_propagate.o libtool: link: ranlib .libs/libghmm.a libtool: link: ( cd ".libs" && rm -f "libghmm.la" && ln -s "../libghmm.la" "libghmm.la" ) make[3]: Leaving directory `/builddir/build/BUILD/ghmm/ghmm' make[2]: Leaving directory `/builddir/build/BUILD/ghmm/ghmm' Making all in tools make[2]: Entering directory `/builddir/build/BUILD/ghmm/tools' make all-recursive make[3]: Entering directory `/builddir/build/BUILD/ghmm/tools' Making all in . make[4]: Entering directory `/builddir/build/BUILD/ghmm/tools' gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT probdist.o -MD -MP -MF .deps/probdist.Tpo -c -o probdist.o probdist.c gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT cluster.o -MD -MP -MF .deps/cluster.Tpo -c -o cluster.o cluster.c gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT scluster.o -MD -MP -MF .deps/scluster.Tpo -c -o scluster.o scluster.c gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT smix_hmm.o -MD -MP -MF .deps/smix_hmm.Tpo -c -o smix_hmm.o smix_hmm.c mv -f .deps/cluster.Tpo .deps/cluster.Po mv -f .deps/scluster.Tpo .deps/scluster.Po gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT smo2xml.o -MD -MP -MF .deps/smo2xml.Tpo -c -o smo2xml.o smo2xml.c /bin/sh ../libtool --tag=CC --mode=link gcc -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -o cluster cluster.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lpthread -lgsl -lgslcblas -lm -lxml2 mv -f .deps/probdist.Tpo .deps/probdist.Po /bin/sh ../libtool --tag=CC --mode=link gcc -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -o scluster scluster.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lpthread -lgsl -lgslcblas -lm -lxml2 mv -f .deps/smix_hmm.Tpo .deps/smix_hmm.Po /bin/sh ../libtool --tag=CC --mode=link gcc -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -o probdist probdist.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lpthread -lgsl -lgslcblas -lm -lxml2 mv -f .deps/smo2xml.Tpo .deps/smo2xml.Po /bin/sh ../libtool --tag=CC --mode=link gcc -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -o smix_hmm smix_hmm.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lpthread -lgsl -lgslcblas -lm -lxml2 libtool: link: gcc -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -o cluster cluster.o ../ghmm/.libs/libghmm.a -lpthread -lgsl -lgslcblas -lm -lxml2 libtool: link: gcc -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -o scluster scluster.o ../ghmm/.libs/libghmm.a -lpthread -lgsl -lgslcblas -lm -lxml2 libtool: link: gcc -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -o probdist probdist.o ../ghmm/.libs/libghmm.a -lpthread -lgsl -lgslcblas -lm -lxml2 libtool: link: gcc -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -o smix_hmm smix_hmm.o ../ghmm/.libs/libghmm.a -lpthread -lgsl -lgslcblas -lm -lxml2 /bin/sh ../libtool --tag=CC --mode=link gcc -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -o smo2xml smo2xml.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lpthread -lgsl -lgslcblas -lm -lxml2 libtool: link: gcc -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -o smo2xml smo2xml.o ../ghmm/.libs/libghmm.a -lpthread -lgsl -lgslcblas -lm -lxml2 make[4]: Leaving directory `/builddir/build/BUILD/ghmm/tools' make[3]: Leaving directory `/builddir/build/BUILD/ghmm/tools' make[2]: Leaving directory `/builddir/build/BUILD/ghmm/tools' Making all in tests make[2]: Entering directory `/builddir/build/BUILD/ghmm/tests' Making all in data make[3]: Entering directory `/builddir/build/BUILD/ghmm/tests/data' Making all in . make[4]: Entering directory `/builddir/build/BUILD/ghmm/tests/data' make[4]: Nothing to be done for `all-am'. make[4]: Leaving directory `/builddir/build/BUILD/ghmm/tests/data' make[3]: Leaving directory `/builddir/build/BUILD/ghmm/tests/data' make[3]: Entering directory `/builddir/build/BUILD/ghmm/tests' gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT randvar_test.o -MD -MP -MF .deps/randvar_test.Tpo -c -o randvar_test.o randvar_test.c gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT root_finder_test.o -MD -MP -MF .deps/root_finder_test.Tpo -c -o root_finder_test.o root_finder_test.c gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT coin_toss_test.o -MD -MP -MF .deps/coin_toss_test.Tpo -c -o coin_toss_test.o coin_toss_test.c gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT two_states_three_symbols.o -MD -MP -MF .deps/two_states_three_symbols.Tpo -c -o two_states_three_symbols.o two_states_three_symbols.c mv -f .deps/root_finder_test.Tpo .deps/root_finder_test.Po gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT libxml-test.o -MD -MP -MF .deps/libxml-test.Tpo -c -o libxml-test.o libxml-test.c mv -f .deps/randvar_test.Tpo .deps/randvar_test.Po gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT chmm.o -MD -MP -MF .deps/chmm.Tpo -c -o chmm.o chmm.c mv -f .deps/two_states_three_symbols.Tpo .deps/two_states_three_symbols.Po gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT chmm_test.o -MD -MP -MF .deps/chmm_test.Tpo -c -o chmm_test.o chmm_test.c mv -f .deps/coin_toss_test.Tpo .deps/coin_toss_test.Po gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT shmm_viterbi_test.o -MD -MP -MF .deps/shmm_viterbi_test.Tpo -c -o shmm_viterbi_test.o shmm_viterbi_test.c mv -f .deps/libxml-test.Tpo .deps/libxml-test.Po gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT test_gsl_ran_gaussian_tail.o -MD -MP -MF .deps/test_gsl_ran_gaussian_tail.Tpo -c -o test_gsl_ran_gaussian_tail.o test_gsl_ran_gaussian_tail.c mv -f .deps/chmm.Tpo .deps/chmm.Po gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT sequences_test.o -MD -MP -MF .deps/sequences_test.Tpo -c -o sequences_test.o sequences_test.c mv -f .deps/chmm_test.Tpo .deps/chmm_test.Po gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT sequences_old_format.o -MD -MP -MF .deps/sequences_old_format.Tpo -c -o sequences_old_format.o sequences_old_format.c mv -f .deps/test_gsl_ran_gaussian_tail.Tpo .deps/test_gsl_ran_gaussian_tail.Po mv -f .deps/shmm_viterbi_test.Tpo .deps/shmm_viterbi_test.Po gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT label_higher_order_test.o -MD -MP -MF .deps/label_higher_order_test.Tpo -c -o label_higher_order_test.o label_higher_order_test.c gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -MT read_fa.o -MD -MP -MF .deps/read_fa.Tpo -c -o read_fa.o read_fa.c mv -f .deps/sequences_test.Tpo .deps/sequences_test.Po /bin/sh ../libtool --tag=CC --mode=link gcc -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -o randvar_test randvar_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lpthread -lgsl -lgslcblas -lm -lxml2 mv -f .deps/sequences_old_format.Tpo .deps/sequences_old_format.Po /bin/sh ../libtool --tag=CC --mode=link gcc -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -o root_finder_test root_finder_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lpthread -lgsl -lgslcblas -lm -lxml2 mv -f .deps/read_fa.Tpo .deps/read_fa.Po /bin/sh ../libtool --tag=CC --mode=link gcc -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -o coin_toss_test coin_toss_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lpthread -lgsl -lgslcblas -lm -lxml2 mv -f .deps/label_higher_order_test.Tpo .deps/label_higher_order_test.Po /bin/sh ../libtool --tag=CC --mode=link gcc -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -o two_states_three_symbols two_states_three_symbols.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lpthread -lgsl -lgslcblas -lm -lxml2 libtool: link: gcc -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -o randvar_test randvar_test.o ../ghmm/.libs/libghmm.a -lpthread -lgsl -lgslcblas -lm -lxml2 libtool: link: gcc -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -o root_finder_test root_finder_test.o ../ghmm/.libs/libghmm.a -lpthread -lgsl -lgslcblas -lm -lxml2 libtool: link: gcc -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -o coin_toss_test coin_toss_test.o ../ghmm/.libs/libghmm.a -lpthread -lgsl -lgslcblas -lm -lxml2 libtool: link: gcc -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -o two_states_three_symbols two_states_three_symbols.o ../ghmm/.libs/libghmm.a -lpthread -lgsl -lgslcblas -lm -lxml2 /bin/sh ../libtool --tag=CC --mode=link gcc -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -o libxml-test libxml-test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lpthread -lgsl -lgslcblas -lm -lxml2 /bin/sh ../libtool --tag=CC --mode=link gcc -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -o chmm chmm.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lpthread -lgsl -lgslcblas -lm -lxml2 /bin/sh ../libtool --tag=CC --mode=link gcc -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -o chmm_test chmm_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lpthread -lgsl -lgslcblas -lm -lxml2 /bin/sh ../libtool --tag=CC --mode=link gcc -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -o shmm_viterbi_test shmm_viterbi_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lpthread -lgsl -lgslcblas -lm -lxml2 libtool: link: gcc -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -o libxml-test libxml-test.o ../ghmm/.libs/libghmm.a -lpthread -lgsl -lgslcblas -lm -lxml2 libtool: link: gcc -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -o chmm chmm.o ../ghmm/.libs/libghmm.a -lpthread -lgsl -lgslcblas -lm -lxml2 libtool: link: gcc -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -o shmm_viterbi_test shmm_viterbi_test.o ../ghmm/.libs/libghmm.a -lpthread -lgsl -lgslcblas -lm -lxml2 libtool: link: gcc -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -o chmm_test chmm_test.o ../ghmm/.libs/libghmm.a -lpthread -lgsl -lgslcblas -lm -lxml2 /bin/sh ../libtool --tag=CC --mode=link gcc -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -o test_gsl_ran_gaussian_tail test_gsl_ran_gaussian_tail.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lpthread -lgsl -lgslcblas -lm -lxml2 /bin/sh ../libtool --tag=CC --mode=link gcc -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -o sequences_test sequences_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lpthread -lgsl -lgslcblas -lm -lxml2 /bin/sh ../libtool --tag=CC --mode=link gcc -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -o sequences_old_format sequences_old_format.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lpthread -lgsl -lgslcblas -lm -lxml2 /bin/sh ../libtool --tag=CC --mode=link gcc -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -o label_higher_order_test label_higher_order_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lpthread -lgsl -lgslcblas -lm -lxml2 libtool: link: gcc -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -o test_gsl_ran_gaussian_tail test_gsl_ran_gaussian_tail.o ../ghmm/.libs/libghmm.a -lpthread -lgsl -lgslcblas -lm -lxml2 libtool: link: gcc -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -o sequences_test sequences_test.o ../ghmm/.libs/libghmm.a -lpthread -lgsl -lgslcblas -lm -lxml2 libtool: link: gcc -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -o sequences_old_format sequences_old_format.o ../ghmm/.libs/libghmm.a -lpthread -lgsl -lgslcblas -lm -lxml2 libtool: link: gcc -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -o label_higher_order_test label_higher_order_test.o ../ghmm/.libs/libghmm.a -lpthread -lgsl -lgslcblas -lm -lxml2 /bin/sh ../libtool --tag=CC --mode=link gcc -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -o read_fa read_fa.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lpthread -lgsl -lgslcblas -lm -lxml2 libtool: link: gcc -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -o read_fa read_fa.o ../ghmm/.libs/libghmm.a -lpthread -lgsl -lgslcblas -lm -lxml2 make[3]: Leaving directory `/builddir/build/BUILD/ghmm/tests' make[2]: Leaving directory `/builddir/build/BUILD/ghmm/tests' Making all in ghmmwrapper make[2]: Entering directory `/builddir/build/BUILD/ghmm/ghmmwrapper' Making all in . make[3]: Entering directory `/builddir/build/BUILD/ghmm/ghmmwrapper' make[3]: Nothing to be done for `all-am'. make[3]: Leaving directory `/builddir/build/BUILD/ghmm/ghmmwrapper' /usr/bin/python setup.py build running build running build_py file ghmmwrapper.py (for module ghmmwrapper) not found creating build creating build/lib.linux-x86_64-2.6 copying ghmm.py -> build/lib.linux-x86_64-2.6 copying ghmmhelper.py -> build/lib.linux-x86_64-2.6 copying modhmmer.py -> build/lib.linux-x86_64-2.6 copying class_change.py -> build/lib.linux-x86_64-2.6 creating build/lib.linux-x86_64-2.6/ghmm_gato copying ghmm_gato/xmlutil.py -> build/lib.linux-x86_64-2.6/ghmm_gato copying ghmm_gato/HMMEd.py -> build/lib.linux-x86_64-2.6/ghmm_gato copying ghmm_gato/__init__.py -> build/lib.linux-x86_64-2.6/ghmm_gato copying ghmm_gato/DataStructures.py -> build/lib.linux-x86_64-2.6/ghmm_gato copying ghmm_gato/GatoGlobals.py -> build/lib.linux-x86_64-2.6/ghmm_gato copying ghmm_gato/GraphUtil.py -> build/lib.linux-x86_64-2.6/ghmm_gato copying ghmm_gato/Graph.py -> build/lib.linux-x86_64-2.6/ghmm_gato copying ghmm_gato/EditObjectAttributesDialog.py -> build/lib.linux-x86_64-2.6/ghmm_gato file ghmmwrapper.py (for module ghmmwrapper) not found running build_ext building '_ghmmwrapper' extension swigging ghmmwrapper.i to ghmmwrapper_wrap.c swig -python -o ghmmwrapper_wrap.c ghmmwrapper.i creating build/temp.linux-x86_64-2.6 gcc -pthread -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -fPIC -I.. -I/usr/include/python2.6 -c sclass_change.c -o build/temp.linux-x86_64-2.6/sclass_change.o -O2 -pipe -Wall gcc -pthread -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -fPIC -I.. -I/usr/include/python2.6 -c pclasschange.c -o build/temp.linux-x86_64-2.6/pclasschange.o -O2 -pipe -Wall gcc -pthread -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -fPIC -I.. -I/usr/include/python2.6 -c gql.c -o build/temp.linux-x86_64-2.6/gql.o -O2 -pipe -Wall gcc -pthread -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 -fPIC -I.. -I/usr/include/python2.6 -c ghmmwrapper_wrap.c -o build/temp.linux-x86_64-2.6/ghmmwrapper_wrap.o -O2 -pipe -Wall ghmmwrapper_wrap.c: In function 'SwigPyObject_richcompare': ghmmwrapper_wrap.c:1519: warning: dereferencing pointer 'res' does break strict-aliasing rules ghmmwrapper_wrap.c:1519: warning: dereferencing pointer 'res' does break strict-aliasing rules ghmmwrapper_wrap.c:1516: note: initialized from here ghmmwrapper_wrap.c:1518: note: initialized from here gcc -pthread -shared -I/usr/include/atlas -I/usr/include -I/usr/include/libxml2 build/temp.linux-x86_64-2.6/sclass_change.o build/temp.linux-x86_64-2.6/pclasschange.o build/temp.linux-x86_64-2.6/gql.o build/temp.linux-x86_64-2.6/ghmmwrapper_wrap.o -L../ghmm/.libs -L/usr/lib64 -lghmm -lm -lpthread -lxml2 -lz -lpython2.6 -o build/lib.linux-x86_64-2.6/_ghmmwrapper.so make[2]: Leaving directory `/builddir/build/BUILD/ghmm/ghmmwrapper' Making all in HMMEd make[2]: Entering directory `/builddir/build/BUILD/ghmm/HMMEd' Making all in . make[3]: Entering directory `/builddir/build/BUILD/ghmm/HMMEd' make[3]: Nothing to be done for `all-am'. make[3]: Leaving directory `/builddir/build/BUILD/ghmm/HMMEd' /usr/bin/python setup.py build running build running build_py creating build creating build/lib copying HMMEditor.py -> build/lib copying ObjectHMM.py -> build/lib copying HMMEditingContext.py -> build/lib running build_scripts creating build/scripts-2.6 copying and adjusting HMMEd -> build/scripts-2.6 changing mode of build/scripts-2.6/HMMEd from 644 to 755 make[2]: Leaving directory `/builddir/build/BUILD/ghmm/HMMEd' make[2]: Entering directory `/builddir/build/BUILD/ghmm' make[2]: Nothing to be done for `all-am'. make[2]: Leaving directory `/builddir/build/BUILD/ghmm' make[1]: Leaving directory `/builddir/build/BUILD/ghmm' + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.SG67Fy + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64 ++ dirname /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64 + cd ghmm + LANG=C + export LANG + unset DISPLAY + rm -rf /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64 + make install DESTDIR=/builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64 Making install in ghmm make[1]: Entering directory `/builddir/build/BUILD/ghmm/ghmm' Making install in . make[2]: Entering directory `/builddir/build/BUILD/ghmm/ghmm' make[3]: Entering directory `/builddir/build/BUILD/ghmm/ghmm' test -z "/usr/lib64" || /bin/mkdir -p "/builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/lib64" /bin/sh ../libtool --mode=install /usr/bin/install -c libghmm.la '/builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/lib64' libtool: install: /usr/bin/install -c .libs/libghmm.so.1.0.0 /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/lib64/libghmm.so.1.0.0 libtool: install: (cd /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/lib64 && { ln -s -f libghmm.so.1.0.0 libghmm.so.1 || { rm -f libghmm.so.1 && ln -s libghmm.so.1.0.0 libghmm.so.1; }; }) libtool: install: (cd /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/lib64 && { ln -s -f libghmm.so.1.0.0 libghmm.so || { rm -f libghmm.so && ln -s libghmm.so.1.0.0 libghmm.so; }; }) libtool: install: /usr/bin/install -c .libs/libghmm.lai /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/lib64/libghmm.la libtool: install: /usr/bin/install -c .libs/libghmm.a /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/lib64/libghmm.a libtool: install: chmod 644 /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/lib64/libghmm.a libtool: install: ranlib /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/lib64/libghmm.a libtool: install: warning: remember to run `libtool --finish /usr/lib64' test -z "/usr/include/ghmm" || /bin/mkdir -p "/builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/include/ghmm" /usr/bin/install -c -m 644 ghmm.h ghmmconfig.h sequence.h psequence.h xmlreader.h xmlwriter.h model.h foba.h viterbi.h gradescent.h kbest.h discrime.h cluster.h scluster.h reestimate.h sfoba.h sviterbi.h smodel.h sdmodel.h sdfoba.h sreestimate.h sgenerate.h smixturehmm.h smap_classify.h pmodel.h pviterbi.h pviterbi_propagate.h rng.h scanner.h obsolete.h unsupported.h '/builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/include/ghmm' make[3]: Leaving directory `/builddir/build/BUILD/ghmm/ghmm' make[2]: Leaving directory `/builddir/build/BUILD/ghmm/ghmm' make[1]: Leaving directory `/builddir/build/BUILD/ghmm/ghmm' Making install in tools make[1]: Entering directory `/builddir/build/BUILD/ghmm/tools' make install-recursive make[2]: Entering directory `/builddir/build/BUILD/ghmm/tools' Making install in . make[3]: Entering directory `/builddir/build/BUILD/ghmm/tools' make[4]: Entering directory `/builddir/build/BUILD/ghmm/tools' test -z "/usr/bin" || /bin/mkdir -p "/builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/bin" /bin/sh ../libtool --mode=install /usr/bin/install -c probdist cluster scluster smix_hmm smo2xml '/builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/bin' libtool: install: /usr/bin/install -c probdist /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/bin/probdist libtool: install: /usr/bin/install -c cluster /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/bin/cluster libtool: install: /usr/bin/install -c scluster /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/bin/scluster libtool: install: /usr/bin/install -c smix_hmm /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/bin/smix_hmm libtool: install: /usr/bin/install -c smo2xml /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/bin/smo2xml test -z "/usr/bin" || /bin/mkdir -p "/builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/bin" /usr/bin/install -c ghmm-config '/builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/bin' make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/builddir/build/BUILD/ghmm/tools' make[3]: Leaving directory `/builddir/build/BUILD/ghmm/tools' make[2]: Leaving directory `/builddir/build/BUILD/ghmm/tools' make[1]: Leaving directory `/builddir/build/BUILD/ghmm/tools' Making install in tests make[1]: Entering directory `/builddir/build/BUILD/ghmm/tests' Making install in data make[2]: Entering directory `/builddir/build/BUILD/ghmm/tests/data' Making install in . make[3]: Entering directory `/builddir/build/BUILD/ghmm/tests/data' make[4]: Entering directory `/builddir/build/BUILD/ghmm/tests/data' make[4]: Nothing to be done for `install-exec-am'. make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/builddir/build/BUILD/ghmm/tests/data' make[3]: Leaving directory `/builddir/build/BUILD/ghmm/tests/data' make[2]: Leaving directory `/builddir/build/BUILD/ghmm/tests/data' make[2]: Entering directory `/builddir/build/BUILD/ghmm/tests' make[3]: Entering directory `/builddir/build/BUILD/ghmm/tests' make[3]: Nothing to be done for `install-exec-am'. make[3]: Nothing to be done for `install-data-am'. make[3]: Leaving directory `/builddir/build/BUILD/ghmm/tests' make[2]: Leaving directory `/builddir/build/BUILD/ghmm/tests' make[1]: Leaving directory `/builddir/build/BUILD/ghmm/tests' Making install in ghmmwrapper make[1]: Entering directory `/builddir/build/BUILD/ghmm/ghmmwrapper' Making all in . make[2]: Entering directory `/builddir/build/BUILD/ghmm/ghmmwrapper' make[2]: Nothing to be done for `all-am'. make[2]: Leaving directory `/builddir/build/BUILD/ghmm/ghmmwrapper' /usr/bin/python setup.py build running build running build_py copying ghmmwrapper.py -> build/lib.linux-x86_64-2.6 running build_ext /usr/bin/python setup.py install -O1 --skip-build --root /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64 running install running install_lib creating /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/lib64/python2.6 creating /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/lib64/python2.6/site-packages copying build/lib.linux-x86_64-2.6/ghmm.py -> /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/lib64/python2.6/site-packages copying build/lib.linux-x86_64-2.6/ghmmhelper.py -> /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/lib64/python2.6/site-packages copying build/lib.linux-x86_64-2.6/modhmmer.py -> /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/lib64/python2.6/site-packages copying build/lib.linux-x86_64-2.6/class_change.py -> /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/lib64/python2.6/site-packages creating /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/lib64/python2.6/site-packages/ghmm_gato copying build/lib.linux-x86_64-2.6/ghmm_gato/xmlutil.py -> /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/lib64/python2.6/site-packages/ghmm_gato copying build/lib.linux-x86_64-2.6/ghmm_gato/HMMEd.py -> /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/lib64/python2.6/site-packages/ghmm_gato copying build/lib.linux-x86_64-2.6/ghmm_gato/__init__.py -> /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/lib64/python2.6/site-packages/ghmm_gato copying build/lib.linux-x86_64-2.6/ghmm_gato/DataStructures.py -> /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/lib64/python2.6/site-packages/ghmm_gato copying build/lib.linux-x86_64-2.6/ghmm_gato/GatoGlobals.py -> /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/lib64/python2.6/site-packages/ghmm_gato copying build/lib.linux-x86_64-2.6/ghmm_gato/GraphUtil.py -> /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/lib64/python2.6/site-packages/ghmm_gato copying build/lib.linux-x86_64-2.6/ghmm_gato/Graph.py -> /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/lib64/python2.6/site-packages/ghmm_gato copying build/lib.linux-x86_64-2.6/ghmm_gato/EditObjectAttributesDialog.py -> /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/lib64/python2.6/site-packages/ghmm_gato copying build/lib.linux-x86_64-2.6/_ghmmwrapper.so -> /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/lib64/python2.6/site-packages copying build/lib.linux-x86_64-2.6/ghmmwrapper.py -> /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/lib64/python2.6/site-packages byte-compiling /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/lib64/python2.6/site-packages/ghmm.py to ghmm.pyc byte-compiling /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/lib64/python2.6/site-packages/ghmmhelper.py to ghmmhelper.pyc byte-compiling /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/lib64/python2.6/site-packages/modhmmer.py to modhmmer.pyc byte-compiling /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/lib64/python2.6/site-packages/class_change.py to class_change.pyc byte-compiling /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/lib64/python2.6/site-packages/ghmm_gato/xmlutil.py to xmlutil.pyc byte-compiling /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/lib64/python2.6/site-packages/ghmm_gato/HMMEd.py to HMMEd.pyc byte-compiling /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/lib64/python2.6/site-packages/ghmm_gato/__init__.py to __init__.pyc byte-compiling /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/lib64/python2.6/site-packages/ghmm_gato/DataStructures.py to DataStructures.pyc byte-compiling /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/lib64/python2.6/site-packages/ghmm_gato/GatoGlobals.py to GatoGlobals.pyc byte-compiling /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/lib64/python2.6/site-packages/ghmm_gato/GraphUtil.py to GraphUtil.pyc byte-compiling /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/lib64/python2.6/site-packages/ghmm_gato/Graph.py to Graph.pyc byte-compiling /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/lib64/python2.6/site-packages/ghmm_gato/EditObjectAttributesDialog.py to EditObjectAttributesDialog.pyc byte-compiling /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/lib64/python2.6/site-packages/ghmmwrapper.py to ghmmwrapper.pyc writing byte-compilation script '/tmp/tmpoXzg6W.py' /usr/bin/python -O /tmp/tmpoXzg6W.py removing /tmp/tmpoXzg6W.py running install_egg_info Writing /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/lib64/python2.6/site-packages/ghmmwrapper-0.8-py2.6.egg-info make[1]: Leaving directory `/builddir/build/BUILD/ghmm/ghmmwrapper' Making install in HMMEd make[1]: Entering directory `/builddir/build/BUILD/ghmm/HMMEd' /usr/bin/python setup.py install -O1 --skip-build --root /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64 running install running install_lib creating /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/lib creating /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/lib/python2.6 creating /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/lib/python2.6/site-packages copying build/lib/HMMEditor.py -> /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/lib/python2.6/site-packages copying build/lib/ObjectHMM.py -> /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/lib/python2.6/site-packages copying build/lib/HMMEditingContext.py -> /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/lib/python2.6/site-packages byte-compiling /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/lib/python2.6/site-packages/HMMEditor.py to HMMEditor.pyc byte-compiling /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/lib/python2.6/site-packages/ObjectHMM.py to ObjectHMM.pyc byte-compiling /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/lib/python2.6/site-packages/HMMEditingContext.py to HMMEditingContext.pyc writing byte-compilation script '/tmp/tmpcImytv.py' /usr/bin/python -O /tmp/tmpcImytv.py removing /tmp/tmpcImytv.py running install_scripts copying build/scripts-2.6/HMMEd -> /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/bin changing mode of /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/bin/HMMEd to 755 running install_egg_info Writing /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/lib/python2.6/site-packages/HMMEd-0.8-py2.6.egg-info make[1]: Leaving directory `/builddir/build/BUILD/ghmm/HMMEd' make[1]: Entering directory `/builddir/build/BUILD/ghmm' make[2]: Entering directory `/builddir/build/BUILD/ghmm' make[2]: Nothing to be done for `install-exec-am'. test -z "/usr/share/ghmm" || /bin/mkdir -p "/builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/share/ghmm" /usr/bin/install -c -m 644 doc/ghmm.dtd.1.0 '/builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/share/ghmm' make[2]: Leaving directory `/builddir/build/BUILD/ghmm' make[1]: Leaving directory `/builddir/build/BUILD/ghmm' + rm -f /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/lib64/libghmm.la + pushd /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/bin ~/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/bin ~/build/BUILD/ghmm + for bin in cluster probdist scluster smix_hmm smo2xml + mv cluster ghmm-cluster + for bin in cluster probdist scluster smix_hmm smo2xml + mv probdist ghmm-probdist + for bin in cluster probdist scluster smix_hmm smo2xml + mv scluster ghmm-scluster + for bin in cluster probdist scluster smix_hmm smo2xml + mv smix_hmm ghmm-smix_hmm + for bin in cluster probdist scluster smix_hmm smo2xml + mv smo2xml ghmm-smo2xml + popd ~/build/BUILD/ghmm + /usr/lib/rpm/find-debuginfo.sh --strict-build-id /builddir/build/BUILD/ghmm extracting debug info from /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/lib64/libghmm.so.1.0.0 extracting debug info from /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/lib64/python2.6/site-packages/_ghmmwrapper.so extracting debug info from /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/bin/ghmm-scluster extracting debug info from /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/bin/ghmm-smix_hmm extracting debug info from /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/bin/ghmm-cluster extracting debug info from /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/bin/ghmm-probdist extracting debug info from /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/bin/ghmm-smo2xml symlinked /usr/lib/debug/usr/lib64/libghmm.so.1.0.0.debug to /usr/lib/debug/usr/lib64/libghmm.so.1.debug symlinked /usr/lib/debug/usr/lib64/libghmm.so.1.0.0.debug to /usr/lib/debug/usr/lib64/libghmm.so.debug 2161 blocks + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-compress + /usr/lib/rpm/redhat/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/redhat/brp-strip-comment-note /usr/bin/strip /usr/bin/objdump + /usr/lib/rpm/brp-python-bytecompile Bytecompiling .py files below /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/lib/python2.6/ using /usr/bin/python2.6 Bytecompiling .py files below /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/lib64/python2.6/ using /usr/bin/python2.6 + /usr/lib/rpm/redhat/brp-python-hardlink + /usr/lib/rpm/redhat/brp-java-repack-jars Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.QegRWU + umask 022 + cd /builddir/build/BUILD + cd ghmm + unset DISPLAY + pushd ghmmwrapper ~/build/BUILD/ghmm/ghmmwrapper ~/build/BUILD/ghmm + popd ~/build/BUILD/ghmm + exit 0 Processing files: ghmm-0.7-4.svn2286.fc13.x86_64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.ulDreh + umask 022 + cd /builddir/build/BUILD + cd ghmm + DOCDIR=/builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/share/doc/ghmm-0.7 + export DOCDIR + rm -rf /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/share/doc/ghmm-0.7 + /bin/mkdir -p /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/share/doc/ghmm-0.7 + cp -pr COPYRIGHT.txt LGPL.txt AUTHORS /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64/usr/share/doc/ghmm-0.7 + exit 0 Provides: _ghmmwrapper.so()(64bit) libghmm.so.1()(64bit) Requires(interp): /sbin/ldconfig /sbin/ldconfig Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PartialHardlinkSets) <= 4.0.4-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires(post): /sbin/ldconfig Requires(postun): /sbin/ldconfig Requires: /usr/bin/python libc.so.6()(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.4)(64bit) libghmm.so.1()(64bit) libgsl.so.0()(64bit) libgslcblas.so.0()(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libpthread.so.0()(64bit) libpthread.so.0(GLIBC_2.2.5)(64bit) libpython2.6.so.1.0()(64bit) libxml2.so.2()(64bit) libxml2.so.2(LIBXML2_2.4.30)(64bit) libxml2.so.2(LIBXML2_2.5.8)(64bit) libxml2.so.2(LIBXML2_2.6.0)(64bit) libxml2.so.2(LIBXML2_2.6.3)(64bit) libxml2.so.2(LIBXML2_2.6.5)(64bit) libz.so.1()(64bit) python(abi) = 2.6 rtld(GNU_HASH) Processing files: ghmm-static-0.7-4.svn2286.fc13.x86_64 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: ghmm-devel-0.7-4.svn2286.fc13.x86_64 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /bin/sh libghmm.so.1()(64bit) Processing files: ghmm-debuginfo-0.7-4.svn2286.fc13.x86_64 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64 warning: Could not canonicalize hostname: x86-1.fedora.phx.redhat.com Wrote: /builddir/build/RPMS/ghmm-0.7-4.svn2286.fc13.x86_64.rpm Wrote: /builddir/build/RPMS/ghmm-static-0.7-4.svn2286.fc13.x86_64.rpm Wrote: /builddir/build/RPMS/ghmm-devel-0.7-4.svn2286.fc13.x86_64.rpm Wrote: /builddir/build/RPMS/ghmm-debuginfo-0.7-4.svn2286.fc13.x86_64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.31FGXE + umask 022 + cd /builddir/build/BUILD + cd ghmm + rm -rf /builddir/build/BUILDROOT/ghmm-0.7-4.svn2286.fc13.x86_64 + exit 0 Child returncode was: 0 LEAVE do -->