------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/pkgconf-1.7.3,1.txz Installing /packages/All/pcre-8.44.txz Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/libffi-3.3_1.txz Installing /packages/All/gettext-runtime-0.21.txz Installing /packages/All/libxml2-2.9.10.txz Installing /packages/All/libiconv-1.16.txz Installing /packages/All/expat-2.2.8.txz Installing /packages/All/ncurses-6.2.20200831.txz Installing /packages/All/readline-8.0.4.txz Installing /packages/All/openssl-1.1.1g,1.txz Installing /packages/All/python37-3.7.9.txz ===== Message from python37-3.7.9: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py37-gdbm databases/py-gdbm@py37 py37-sqlite3 databases/py-sqlite3@py37 py37-tkinter x11-toolkits/py-tkinter@py37 Installing /packages/All/glib-2.56.3_9,1.txz No schema files found: doing nothing. SUCCEEDED 00:00:18 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> exonerate-2.4.0 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> exonerate-2.4.0 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by exonerate-2.4.0 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> exonerate-2.4.0 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by exonerate-2.4.0 for building => SHA256 Checksum OK for exonerate-2.4.0.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> exonerate-2.4.0 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by exonerate-2.4.0 for building ===> Extracting for exonerate-2.4.0 => SHA256 Checksum OK for exonerate-2.4.0.tar.gz. Extracted Memory Use: 3.43M SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for exonerate-2.4.0 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> exonerate-2.4.0 depends on package: pkgconf>=1.3.0_1 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- ===> exonerate-2.4.0 depends on shared library: libglib-2.0.so - found (/usr/local/lib/libglib-2.0.so) ===> exonerate-2.4.0 depends on shared library: libintl.so - found (/usr/local/lib/libintl.so) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> exonerate-2.4.0 depends on package: pkgconf>=1.3.0_1 - found ===> exonerate-2.4.0 depends on shared library: libglib-2.0.so - found (/usr/local/lib/libglib-2.0.so) ===> exonerate-2.4.0 depends on shared library: libintl.so - found (/usr/local/lib/libintl.so) ===> Configuring for exonerate-2.4.0 configure: loading site script /xports/Templates/config.site checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking whether make sets $(MAKE)... yes checking for working aclocal-1.4... missing checking for working autoconf... missing checking for working automake-1.4... missing checking for working autoheader... missing checking for working makeinfo... missing checking for gcc... cc 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 cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for a BSD-compatible install... /usr/bin/install -c checking whether make sets $(MAKE)... (cached) yes checking for an ANSI C-conforming const... yes checking for inline... inline checking how to run the C preprocessor... cpp checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep checking for ANSI C header files... (cached) yes checking for sys/types.h... (cached) yes checking for sys/stat.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for memory.h... (cached) yes checking for strings.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for unistd.h... (cached) yes checking for limits.h... (cached) yes checking for errno.h... (cached) yes checking for math.h... (cached) yes checking for strings.h... (cached) yes checking for ctype.h... (cached) yes checking for sys/stat.h... (cached) yes checking for sys/types.h... (cached) yes checking for time.h... (cached) yes checking for unistd.h... (cached) yes checking build system type... x86_64-portbld-dragonfly5.9 checking host system type... x86_64-portbld-dragonfly5.9 Set host to x86_64-portbld-dragonfly5.9 x86_64-portbld-dragonfly5.9 Customising build for X86_64 Set source_root_dir to /construction/biology/exonerate/exonerate-2.4.0 ---------------------------------------------------------------- checking for socklen_t... yes checking for pkg-config... /usr/local/bin/pkg-config Using GLIB-2 Turning assertions off Turning paranoid options off Not using options for profiling with gprof Not using options for analysis with gcov Adding support for LARGE FILES (>2Gb) for a 32 bit system Using COMPILED C4 MODELS Installing UTILITIES Using PTHREADS ---------------------------------------------------------------- configure: creating ./config.status config.status: creating Makefile config.status: creating doc/Makefile config.status: creating doc/man/Makefile config.status: creating doc/man/man1/Makefile config.status: creating src/Makefile config.status: creating src/general/Makefile config.status: creating src/sequence/Makefile config.status: creating src/database/Makefile config.status: creating src/struct/Makefile config.status: creating src/comparison/Makefile config.status: creating src/c4/Makefile config.status: creating src/bsdp/Makefile config.status: creating src/sdp/Makefile config.status: creating src/hub/Makefile config.status: creating src/model/Makefile config.status: creating src/program/Makefile config.status: creating src/util/Makefile config.status: creating test/Makefile config.status: creating test/util/Makefile config.status: creating test/ipcress/Makefile config.status: creating test/exonerate/Makefile config.status: creating test/data/Makefile config.status: creating test/data/cdna/Makefile config.status: creating test/data/protein/Makefile SUCCEEDED 00:00:05 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for exonerate-2.4.0 Making all in doc Making all in man Making all in man1 Making all in src Making all in struct cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fsm.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fsm.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c recyclebin.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fsm.test fsm.test.o fsm.o recyclebin.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c matrix.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c matrix.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o matrix.test matrix.test.o matrix.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c pqueue.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c pqueue.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o pqueue.test pqueue.test.o pqueue.o recyclebin.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c slist.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c slist.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o slist.test slist.test.o slist.o recyclebin.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c rangetree.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c rangetree.c rangetree.c: In function 'RangeTree_insert_recent': rangetree.c:151:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] g_tree_traverse(rt->recent_data, RangeTree_insert_recent_collect, ^~~~~~~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:88, from rangetree.h:23, from rangetree.c:18: /usr/local/include/glib-2.0/glib/gtree.h:88:10: note: declared here void g_tree_traverse (GTree *tree, ^~~~~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o rangetree.test rangetree.test.o rangetree.o recyclebin.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c vfsm.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c vfsm.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o vfsm.test vfsm.test.o vfsm.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c recyclebin.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o recyclebin.test recyclebin.test.o recyclebin.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c sparsecache.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c sparsecache.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o sparsecache.test sparsecache.test.o sparsecache.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c dejavu.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c dejavu.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o dejavu.test dejavu.test.o dejavu.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c bitarray.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c bitarray.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o bitarray.test bitarray.test.o bitarray.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c splaytree.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c splaytree.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o splaytree.test splaytree.test.o splaytree.o recyclebin.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c noitree.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c noitree.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o noitree.test noitree.test.o noitree.o recyclebin.o splaytree.o -L/usr/local/lib -lglib-2.0 -lintl Making all in general cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c argument.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c argument.c argument.c: In function 'ArgumentParse_boolean': argument.c:138:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(arg_string, true_string[i])) ^~ In file included from /usr/local/include/glib-2.0/glib.h:79, from argument.h:26, from argument.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ argument.c:140:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(arg_string, false_string[i])) ^~ In file included from /usr/local/include/glib-2.0/glib.h:79, from argument.h:26, from argument.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ argument.c: In function 'main': argument.c:307:9: warning: 'g_thread_init' is deprecated [-Wdeprecated-declarations] g_thread_init(NULL); ^~~~~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:108, from argument.h:26, from argument.c:16: /usr/local/include/glib-2.0/glib/deprecated/gthread.h:265:10: note: declared here void g_thread_init (gpointer vtable); ^~~~~~~~~~~~~ argument.c: In function 'Argument_process': argument.c:502:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] g_tree_traverse(arg->option_registry, Argument_set_env_var_func, ^~~~~~~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:88, from argument.h:26, from argument.c:16: /usr/local/include/glib-2.0/glib/gtree.h:88:10: note: declared here void g_tree_traverse (GTree *tree, ^~~~~~~~~~~~~~~ argument.c:559:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] g_tree_traverse(arg->option_registry, ^~~~~~~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:88, from argument.h:26, from argument.c:16: /usr/local/include/glib-2.0/glib/gtree.h:88:10: note: declared here void g_tree_traverse (GTree *tree, ^~~~~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o argument.test argument.test.o argument.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c lineparse.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c lineparse.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o lineparse.test lineparse.test.o lineparse.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c compoundfile.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c compoundfile.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o compoundfile.test compoundfile.test.o compoundfile.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c socket.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c socket.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o socket.test socket.test.o socket.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c jobqueue.test.c jobqueue.test.c: In function 'main': jobqueue.test.c:35:9: warning: 'g_thread_init' is deprecated [-Wdeprecated-declarations] g_thread_init(NULL); ^~~~~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:108, from jobqueue.h:23, from jobqueue.test.c:17: /usr/local/include/glib-2.0/glib/deprecated/gthread.h:265:10: note: declared here void g_thread_init (gpointer vtable); ^~~~~~~~~~~~~ cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c jobqueue.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o jobqueue.test jobqueue.test.o jobqueue.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c threadref.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c threadref.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o threadref.test threadref.test.o threadref.o -lpthread -L/usr/local/lib -lglib-2.0 -lintl Making all in sequence cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c sequence.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c sequence.c sequence.c: In function 'Sequence_destroy_annotation_tree': sequence.c:97:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] g_tree_traverse(tree, Sequence_destroy_annotation_data, ^~~~~~~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:88, from sequence.h:24, from sequence.c:21: /usr/local/include/glib-2.0/glib/gtree.h:88:10: note: declared here void g_tree_traverse (GTree *tree, ^~~~~~~~~~~~~~~ cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c alphabet.c alphabet.c: In function 'Alphabet_name_get_type': alphabet.c:317:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(name, dna_string[i])) ^~ In file included from /usr/local/include/glib-2.0/glib.h:79, from alphabet.h:24, from alphabet.c:19: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ alphabet.c:320:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(name, protein_string[i])) ^~ In file included from /usr/local/include/glib-2.0/glib.h:79, from alphabet.h:24, from alphabet.c:19: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ alphabet.c:323:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(name, unknown_string[i])) ^~ In file included from /usr/local/include/glib-2.0/glib.h:79, from alphabet.h:24, from alphabet.c:19: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c translate.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c splice.c splice.c: In function 'SplicePredictor_parse_data': splice.c:146:17: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(word, "splice")) ^~ In file included from /usr/local/include/glib-2.0/glib.h:79, from splice.h:23, from splice.c:22: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ splice.c: In function 'SplicePredictor_add_5SS_data': splice.c:195:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if((!path) || (!strlen(path)) || (!g_strcasecmp(path, "primate"))) ^~ In file included from /usr/local/include/glib-2.0/glib.h:79, from splice.h:23, from splice.c:22: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ splice.c: In function 'SplicePredictor_add_3SS_data': splice.c:203:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if((!path) || (!strlen(path)) || (!g_strcasecmp(path, "primate"))) ^~ In file included from /usr/local/include/glib-2.0/glib.h:79, from splice.h:23, from splice.c:22: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o sequence.test sequence.test.o sequence.o alphabet.o translate.o splice.o ../../src/struct/matrix.o ../../src/struct/sparsecache.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c submat.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c submat.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o submat.test submat.test.o submat.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c translate.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o translate.test translate.test.o translate.o ../../src/general/argument.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c splice.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o splice.test splice.test.o splice.o ../../src/struct/matrix.o ../../src/struct/sparsecache.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c alphabet.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o alphabet.test alphabet.test.o alphabet.o ../../src/general/argument.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c codonsubmat.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c codonsubmat.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o codonsubmat.test codonsubmat.test.o codonsubmat.o ../../src/general/argument.o -lm -L/usr/local/lib -lglib-2.0 -lintl Making all in comparison cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c wordhood.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c wordhood.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o wordhood.test wordhood.test.o wordhood.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c hspset.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c hspset.c hspset.c: In function 'HSP_Display_insert': hspset.c:637:9: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] g_strdown(query_str); ^~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:79, from hspset.h:26, from hspset.c:20: /usr/local/include/glib-2.0/glib/gstrfuncs.h:208:23: note: declared here gchar* g_strdown (gchar *string); ^~~~~~~~~ hspset.c:638:9: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] g_strdown(target_str); ^~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:79, from hspset.h:26, from hspset.c:20: /usr/local/include/glib-2.0/glib/gstrfuncs.h:208:23: note: declared here gchar* g_strdown (gchar *string); ^~~~~~~~~ hspset.c:640:9: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] g_strup(query_str); ^~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:79, from hspset.h:26, from hspset.c:20: /usr/local/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here gchar* g_strup (gchar *string); ^~~~~~~ hspset.c:641:9: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] g_strup(target_str); ^~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:79, from hspset.h:26, from hspset.c:20: /usr/local/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here gchar* g_strup (gchar *string); ^~~~~~~ cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c match.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o hspset.test hspset.test.o hspset.o match.o wordhood.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/general/threadref.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c pcr.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c pcr.c pcr.c: In function 'PCR_Match_allocate': pcr.c:31:9: warning: 'g_mem_chunk_alloc' is deprecated [-Wdeprecated-declarations] pcr_match = g_chunk_new(PCR_Match, pcr->match_mem_chunk); ^~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:103, from pcr.h:23, from pcr.c:16: /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:50:17: note: declared here gpointer g_mem_chunk_alloc (GMemChunk *mem_chunk); ^~~~~~~~~~~~~~~~~ pcr.c: In function 'PCR_Probe_create': pcr.c:59:5: warning: 'g_mem_chunk_alloc' is deprecated [-Wdeprecated-declarations] register PCR_Probe *pcr_probe = g_chunk_new(PCR_Probe, ^~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:103, from pcr.h:23, from pcr.c:16: /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:50:17: note: declared here gpointer g_mem_chunk_alloc (GMemChunk *mem_chunk); ^~~~~~~~~~~~~~~~~ pcr.c: In function 'PCR_Probe_destroy': pcr.c:69:5: warning: 'g_mem_chunk_free' is deprecated [-Wdeprecated-declarations] g_mem_chunk_free(pcr->probe_mem_chunk, pcr_probe); ^~~~~~~~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:103, from pcr.h:23, from pcr.c:16: /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:54:17: note: declared here void g_mem_chunk_free (GMemChunk *mem_chunk, ^~~~~~~~~~~~~~~~ pcr.c: In function 'PCR_Sensor_create': pcr.c:155:5: warning: 'g_mem_chunk_alloc' is deprecated [-Wdeprecated-declarations] register PCR_Sensor *pcr_sensor = g_chunk_new(PCR_Sensor, ^~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:103, from pcr.h:23, from pcr.c:16: /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:50:17: note: declared here gpointer g_mem_chunk_alloc (GMemChunk *mem_chunk); ^~~~~~~~~~~~~~~~~ pcr.c: In function 'PCR_Sensor_destroy': pcr.c:174:5: warning: 'g_mem_chunk_free' is deprecated [-Wdeprecated-declarations] g_mem_chunk_free(pcr->sensor_mem_chunk, pcr_sensor); ^~~~~~~~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:103, from pcr.h:23, from pcr.c:16: /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:54:17: note: declared here void g_mem_chunk_free (GMemChunk *mem_chunk, ^~~~~~~~~~~~~~~~ pcr.c: In function 'PCR_Primer_create': pcr.c:252:5: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] g_strup(pcr_primer->forward); ^~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:79, from pcr.h:23, from pcr.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here gchar* g_strup (gchar *string); ^~~~~~~ pcr.c:253:5: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] g_strup(pcr_primer->revcomp); ^~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:79, from pcr.h:23, from pcr.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here gchar* g_strup (gchar *string); ^~~~~~~ pcr.c: In function 'PCR_create': pcr.c:357:5: warning: 'g_mem_chunk_new' is deprecated [-Wdeprecated-declarations] pcr->sensor_mem_chunk = g_mem_chunk_new("PCR_Sensor", ^~~ In file included from /usr/local/include/glib-2.0/glib.h:103, from pcr.h:23, from pcr.c:16: /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:43:17: note: declared here GMemChunk * g_mem_chunk_new (const gchar *name, ^~~~~~~~~~~~~~~ pcr.c:363:5: warning: 'g_mem_chunk_new' is deprecated [-Wdeprecated-declarations] pcr->probe_mem_chunk = g_mem_chunk_new("PCR_Probe", ^~~ In file included from /usr/local/include/glib-2.0/glib.h:103, from pcr.h:23, from pcr.c:16: /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:43:17: note: declared here GMemChunk * g_mem_chunk_new (const gchar *name, ^~~~~~~~~~~~~~~ pcr.c:366:5: warning: 'g_mem_chunk_new' is deprecated [-Wdeprecated-declarations] pcr->match_mem_chunk = g_mem_chunk_new("PCR_Match", ^~~ In file included from /usr/local/include/glib-2.0/glib.h:103, from pcr.h:23, from pcr.c:16: /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:43:17: note: declared here GMemChunk * g_mem_chunk_new (const gchar *name, ^~~~~~~~~~~~~~~ pcr.c: In function 'PCR_destroy': pcr.c:381:5: warning: 'g_mem_chunk_destroy' is deprecated [-Wdeprecated-declarations] g_mem_chunk_destroy(pcr->sensor_mem_chunk); ^~~~~~~~~~~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:103, from pcr.h:23, from pcr.c:16: /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:48:17: note: declared here void g_mem_chunk_destroy (GMemChunk *mem_chunk); ^~~~~~~~~~~~~~~~~~~ pcr.c:383:5: warning: 'g_mem_chunk_destroy' is deprecated [-Wdeprecated-declarations] g_mem_chunk_destroy(pcr->probe_mem_chunk); ^~~~~~~~~~~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:103, from pcr.h:23, from pcr.c:16: /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:48:17: note: declared here void g_mem_chunk_destroy (GMemChunk *mem_chunk); ^~~~~~~~~~~~~~~~~~~ pcr.c:384:5: warning: 'g_mem_chunk_destroy' is deprecated [-Wdeprecated-declarations] g_mem_chunk_destroy(pcr->match_mem_chunk); ^~~~~~~~~~~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:103, from pcr.h:23, from pcr.c:16: /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:48:17: note: declared here void g_mem_chunk_destroy (GMemChunk *mem_chunk); ^~~~~~~~~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o pcr.test pcr.test.o pcr.o wordhood.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/struct/fsm.o ../../src/struct/slist.o ../../src/struct/recyclebin.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c comparison.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c comparison.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o comparison.test comparison.test.o comparison.o hspset.o match.o wordhood.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/struct/recyclebin.o ../../src/struct/pqueue.o ../../src/general/threadref.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c match.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o match.test match.test.o match.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c seeder.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c seeder.c seeder.c: In function 'Seeder_decide_fsm_type': seeder.c:268:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(force_fsm, "none")) ^~ In file included from /usr/local/include/glib-2.0/glib.h:79, from seeder.h:23, from seeder.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ seeder.c:273:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(force_fsm, "normal")) ^~ In file included from /usr/local/include/glib-2.0/glib.h:79, from seeder.h:23, from seeder.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ seeder.c:275:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(force_fsm, "compact")) ^~ In file included from /usr/local/include/glib-2.0/glib.h:79, from seeder.h:23, from seeder.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o seeder.test seeder.test.o seeder.o wordhood.o hspset.o match.o comparison.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/struct/recyclebin.o ../../src/struct/fsm.o ../../src/struct/vfsm.o ../../src/struct/pqueue.o ../../src/general/threadref.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl Making all in database cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastadb.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastadb.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastadb.test fastadb.test.o fastadb.o ../../src/general/compoundfile.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastapipe.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastapipe.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastapipe.test fastapipe.test.o fastapipe.o fastadb.o ../../src/general/compoundfile.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c dataset.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c dataset.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o dataset.test dataset.test.o dataset.o fastadb.o ../../src/general/compoundfile.o ../../src/struct/bitarray.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c index.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c index.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o index.test index.test.o index.o fastadb.o dataset.o ../../src/general/compoundfile.o ../../src/general/threadref.o ../../src/struct/bitarray.o ../../src/struct/vfsm.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/struct/splaytree.o ../../src/struct/noitree.o ../../src/comparison/wordhood.o ../../src/comparison/hspset.o ../../src/comparison/match.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl Making all in c4 cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c region.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c region.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o region.test region.test.o region.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c c4.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c c4.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o c4.test c4.test.o c4.o region.o ../../src/struct/matrix.o ../../src/general/threadref.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c alignment.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c alignment.c alignment.c: In function 'AlignmentView_add_SPLICE_SITE': alignment.c:660:9: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] g_strdown(qy_seq_string); ^~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:79, from ../../src/comparison/match.h:23, from alignment.c:20: /usr/local/include/glib-2.0/glib/gstrfuncs.h:208:23: note: declared here gchar* g_strdown (gchar *string); ^~~~~~~~~ alignment.c:667:9: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] g_strdown(tg_seq_string); ^~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:79, from ../../src/comparison/match.h:23, from alignment.c:20: /usr/local/include/glib-2.0/glib/gstrfuncs.h:208:23: note: declared here gchar* g_strdown (gchar *string); ^~~~~~~~~ alignment.c:677:13: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] g_strdown(qy_seq_string); ^~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:79, from ../../src/comparison/match.h:23, from alignment.c:20: /usr/local/include/glib-2.0/glib/gstrfuncs.h:208:23: note: declared here gchar* g_strdown (gchar *string); ^~~~~~~~~ alignment.c:690:9: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] g_strdown(tg_seq_string); ^~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:79, from ../../src/comparison/match.h:23, from alignment.c:20: /usr/local/include/glib-2.0/glib/gstrfuncs.h:208:23: note: declared here gchar* g_strdown (gchar *string); ^~~~~~~~~ alignment.c: In function 'AlignmentView_add_SPLIT_CODON': alignment.c:987:5: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] g_strup(qy_codon); ^~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:79, from ../../src/comparison/match.h:23, from alignment.c:20: /usr/local/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here gchar* g_strup (gchar *string); ^~~~~~~ alignment.c:988:5: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] g_strup(tg_codon); ^~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:79, from ../../src/comparison/match.h:23, from alignment.c:20: /usr/local/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here gchar* g_strup (gchar *string); ^~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o alignment.test alignment.test.o alignment.o c4.o region.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/general/threadref.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c codegen.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c codegen.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o codegen.test codegen.test.o codegen.o ../../src/general/argument.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c optimal.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c optimal.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c layout.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c viterbi.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c subopt.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c cgutil.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o optimal.test optimal.test.o optimal.o c4.o alignment.o codegen.o region.o layout.o viterbi.o subopt.o cgutil.o ../../src/struct/slist.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/general/threadref.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c layout.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o layout.test layout.test.o layout.o ../../src/struct/matrix.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c viterbi.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o viterbi.test viterbi.test.o viterbi.o c4.o region.o alignment.o codegen.o layout.o subopt.o cgutil.o ../../src/struct/slist.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/general/threadref.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c opair.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c opair.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o opair.test opair.test.o opair.o optimal.o c4.o alignment.o codegen.o region.o layout.o viterbi.o subopt.o cgutil.o ../../src/struct/slist.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/general/threadref.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c subopt.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o subopt.test subopt.test.o subopt.o region.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c cgutil.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o cgutil.test cgutil.test.o cgutil.o codegen.o c4.o region.o ../../src/general/argument.o ../../src/struct/matrix.o ../../src/general/threadref.o -L/usr/local/lib -lglib-2.0 -lintl Making all in bsdp cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c heuristic.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c heuristic.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o heuristic.test heuristic.test.o heuristic.o ../../src/struct/slist.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/c4/c4.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/codegen.o ../../src/c4/region.o ../../src/c4/layout.o ../../src/c4/viterbi.o ../../src/c4/subopt.o ../../src/c4/cgutil.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c bsdp.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c bsdp.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o bsdp.test bsdp.test.o bsdp.o ../../src/general/argument.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c hpair.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c hpair.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c sar.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o hpair.test hpair.test.o hpair.o heuristic.o bsdp.o sar.o ../../src/struct/slist.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/comparison/hspset.o ../../src/comparison/wordhood.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/c4/c4.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/codegen.o ../../src/c4/region.o ../../src/c4/layout.o ../../src/c4/viterbi.o ../../src/c4/subopt.o ../../src/c4/cgutil.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c sar.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o sar.test sar.test.o sar.o heuristic.o ../../src/struct/slist.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/c4/c4.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/codegen.o ../../src/c4/region.o ../../src/c4/layout.o ../../src/c4/viterbi.o ../../src/c4/subopt.o ../../src/c4/cgutil.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl Making all in sdp cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c sdp.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c sdp.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c boundary.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c scheduler.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c lookahead.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c straceback.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o sdp.test sdp.test.o sdp.o boundary.o scheduler.o lookahead.o straceback.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/comparison/hspset.o ../../src/comparison/comparison.o ../../src/comparison/wordhood.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/c4/c4.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/codegen.o ../../src/c4/region.o ../../src/c4/layout.o ../../src/c4/viterbi.o ../../src/c4/subopt.o ../../src/c4/cgutil.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c lookahead.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o lookahead.test lookahead.test.o lookahead.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c boundary.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o boundary.test boundary.test.o boundary.o ../../src/general/argument.o ../../src/c4/region.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c scheduler.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o scheduler.test scheduler.test.o scheduler.o lookahead.o boundary.o straceback.o ../../src/struct/recyclebin.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/c4/c4.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/codegen.o ../../src/c4/region.o ../../src/c4/layout.o ../../src/c4/viterbi.o ../../src/c4/subopt.o ../../src/c4/cgutil.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c straceback.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o straceback.test straceback.test.o straceback.o ../../src/struct/recyclebin.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/c4/c4.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/codegen.o ../../src/c4/region.o ../../src/c4/layout.o ../../src/c4/viterbi.o ../../src/c4/subopt.o ../../src/c4/cgutil.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl Making all in model cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c edit_distance.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c edit_distance.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o edit_distance.test edit_distance.test.o edit_distance.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c affine.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c affine.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c ungapped.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o affine.test affine.test.o affine.o ungapped.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c protein2dna.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c protein2dna.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c frameshift.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o protein2dna.test protein2dna.test.o protein2dna.o affine.o ungapped.o frameshift.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c ner.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c ner.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o ner.test ner.test.o ner.o affine.o ungapped.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c est2genome.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c est2genome.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c intron.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o est2genome.test est2genome.test.o est2genome.o affine.o ungapped.o intron.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c ungapped.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o ungapped.test ungapped.test.o ungapped.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c intron.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o intron.test intron.test.o intron.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c protein2genome.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c protein2genome.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c phase.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o protein2genome.test protein2genome.test.o protein2genome.o protein2dna.o ungapped.o intron.o affine.o frameshift.o phase.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c coding2coding.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c coding2coding.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o coding2coding.test coding2coding.test.o coding2coding.o affine.o ungapped.o frameshift.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c frameshift.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o frameshift.test frameshift.test.o frameshift.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c coding2genome.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c coding2genome.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o coding2genome.test coding2genome.test.o coding2genome.o coding2coding.o affine.o ungapped.o frameshift.o intron.o phase.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c cdna2genome.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c cdna2genome.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o cdna2genome.test cdna2genome.test.o cdna2genome.o affine.o ungapped.o frameshift.o intron.o phase.o coding2coding.o coding2genome.o est2genome.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c genome2genome.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c genome2genome.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o genome2genome.test genome2genome.test.o genome2genome.o coding2coding.o affine.o ungapped.o frameshift.o intron.o phase.o coding2genome.o cdna2genome.o est2genome.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c phase.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o phase.test phase.test.o phase.o intron.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c modeltype.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c modeltype.c modeltype.c: In function 'Model_Type_from_string': modeltype.c:121:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(name[i], str)) ^~ In file included from /usr/local/include/glib-2.0/glib.h:79, from ../../src/c4/c4.h:23, from modeltype.h:23, from modeltype.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ modeltype.c:124:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(short_name[i], str)) ^~ In file included from /usr/local/include/glib-2.0/glib.h:79, from ../../src/c4/c4.h:23, from modeltype.h:23, from modeltype.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o modeltype.test modeltype.test.o modeltype.o ungapped.o affine.o est2genome.o ner.o protein2dna.o protein2genome.o coding2coding.o coding2genome.o genome2genome.o cdna2genome.o frameshift.o phase.o intron.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c bootstrapper.c bootstrapper.c: In function 'Argument_main': bootstrapper.c:421:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if((!models) || (!g_strcasecmp(models, "all"))) ^~ In file included from /usr/local/include/glib-2.0/glib.h:79, from ../../src/c4/c4.h:23, from ungapped.h:23, from bootstrapper.c:20: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o bootstrapper bootstrapper.o modeltype.o ungapped.o affine.o est2genome.o ner.o protein2dna.o protein2genome.o coding2coding.o coding2genome.o genome2genome.o cdna2genome.o frameshift.o intron.o phase.o ../../src/struct/pqueue.o ../../src/comparison/comparison.o ../../src/comparison/hspset.o ../../src/comparison/wordhood.o ../../src/bsdp/heuristic.o ../../src/sdp/sdp.o ../../src/sdp/scheduler.o ../../src/sdp/straceback.o ../../src/sdp/lookahead.o ../../src/sdp/boundary.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl Making all in hub cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/general -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c gam.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/general -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c gam.c gam.c: In function 'GAM_Refinement_from_string': gam.c:68:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(name[i], str)) ^~ In file included from /usr/local/include/glib-2.0/glib.h:79, from gam.h:23, from gam.c:21: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ gam.c: In function 'GAM_bestn_tree_destroy': gam.c:526:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] g_tree_traverse(bestn_tree, GAM_tree_collect_values, ^~~~~~~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:88, from gam.h:23, from gam.c:21: /usr/local/include/glib-2.0/glib/gtree.h:88:10: note: declared here void g_tree_traverse (GTree *tree, ^~~~~~~~~~~~~~~ gam.c: In function 'GAM_percent_threshold_tree_destroy': gam.c:539:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] g_tree_traverse(percent_threshold_tree, GAM_tree_collect_values, ^~~~~~~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:88, from gam.h:23, from gam.c:21: /usr/local/include/glib-2.0/glib/gtree.h:88:10: note: declared here void g_tree_traverse (GTree *tree, ^~~~~~~~~~~~~~~ gam.c: In function 'GAM_report': gam.c:589:9: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] g_tree_traverse(gam->bestn_tree, GAM_bestn_tree_report_traverse, ^~~~~~~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:88, from gam.h:23, from gam.c:21: /usr/local/include/glib-2.0/glib/gtree.h:88:10: note: declared here void g_tree_traverse (GTree *tree, ^~~~~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o gam.test gam.test.o gam.o ../../src/comparison/hspset.o ../../src/comparison/comparison.o ../../src/comparison/wordhood.o ../../src/struct/sparsecache.o ../../src/general/compoundfile.o ../../src/general/threadref.o ../../src/c4/c4.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/opair.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/region.o ../../src/c4/subopt.o ../../src/bsdp/bsdp.o ../../src/bsdp/sar.o ../../src/bsdp/heuristic.o ../../src/bsdp/hpair.o ../../src/sdp/boundary.o ../../src/sdp/sdp.o ../../src/sdp/scheduler.o ../../src/sdp/straceback.o ../../src/sdp/lookahead.o ../../src/struct/matrix.o ../../src/struct/slist.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/translate.o ../../src/sequence/splice.o ../../src/model/affine.o ../../src/model/est2genome.o ../../src/model/ner.o ../../src/model/protein2dna.o ../../src/model/protein2genome.o ../../src/model/coding2coding.o ../../src/model/coding2genome.o ../../src/model/cdna2genome.o ../../src/model/genome2genome.o ../../src/model/ungapped.o ../../src/model/intron.o ../../src/model/frameshift.o ../../src/model/phase.o ../../src/model/modeltype.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/jobqueue.o ../../src/comparison/match.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/general -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c analysis.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/general -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c analysis.c analysis.c: In function 'Analysis_decide_scan_query': analysis.c:329:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(force_scan, "none")){ ^~ In file included from /usr/local/include/glib-2.0/glib.h:79, from analysis.h:23, from analysis.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ analysis.c:336:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] } else if((!g_strcasecmp(force_scan, "query")) ^ In file included from /usr/local/include/glib-2.0/glib.h:79, from analysis.h:23, from analysis.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ analysis.c:337:12: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] || (!g_strcasecmp(force_scan, "q"))){ ^~ In file included from /usr/local/include/glib-2.0/glib.h:79, from analysis.h:23, from analysis.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ analysis.c:339:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] } else if((!g_strcasecmp(force_scan, "target")) ^ In file included from /usr/local/include/glib-2.0/glib.h:79, from analysis.h:23, from analysis.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ analysis.c:340:12: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] || (!g_strcasecmp(force_scan, "t"))){ ^~ In file included from /usr/local/include/glib-2.0/glib.h:79, from analysis.h:23, from analysis.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/general -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c bsam.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o analysis.test analysis.test.o analysis.o gam.o bsam.o ../../src/comparison/hspset.o ../../src/comparison/wordhood.o ../../src/comparison/seeder.o ../../src/comparison/comparison.o ../../src/database/fastapipe.o ../../src/database/fastadb.o ../../src/struct/dejavu.o ../../src/struct/fsm.o ../../src/struct/vfsm.o ../../src/struct/sparsecache.o ../../src/general/compoundfile.o ../../src/general/socket.o ../../src/general/threadref.o ../../src/c4/c4.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/opair.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/region.o ../../src/c4/subopt.o ../../src/bsdp/bsdp.o ../../src/bsdp/sar.o ../../src/bsdp/heuristic.o ../../src/bsdp/hpair.o ../../src/sdp/boundary.o ../../src/sdp/sdp.o ../../src/sdp/scheduler.o ../../src/sdp/straceback.o ../../src/sdp/lookahead.o ../../src/struct/matrix.o ../../src/struct/slist.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/translate.o ../../src/sequence/splice.o ../../src/model/affine.o ../../src/model/est2genome.o ../../src/model/ner.o ../../src/model/protein2dna.o ../../src/model/protein2genome.o ../../src/model/coding2coding.o ../../src/model/coding2genome.o ../../src/model/cdna2genome.o ../../src/model/genome2genome.o ../../src/model/ungapped.o ../../src/model/intron.o ../../src/model/frameshift.o ../../src/model/phase.o ../../src/model/modeltype.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/jobqueue.o ../../src/comparison/match.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/general -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c bsam.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o bsam.test bsam.test.o bsam.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o ../../src/comparison/hspset.o ../../src/comparison/comparison.o ../../src/comparison/match.o ../../src/comparison/wordhood.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/translate.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/sequence/splice.o ../../src/struct/dejavu.o ../../src/struct/pqueue.o ../../src/struct/sparsecache.o ../../src/struct/recyclebin.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl Making all in program cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/hub -I../../src/general -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c exonerate.c ../../src/model/bootstrapper --compiled no ** Message: 22:59:18.081: Starting building bootstrapping components ** Message: 22:59:18.082: Processing model [u] ** Message: 22:59:18.083: Bootstrapper processing model [ungapped:dna2dna] ** Message: 22:59:18.083: Process optimal [optimal:ungapped:dna2dna] ** (process:666679): WARNING **: 22:59:18.083: Creating codegen directory [/construction/biology/exonerate/exonerate-2.4.0/codegen] ** (process:666679): WARNING **: 22:59:18.083: Creating codegen directory [/construction/biology/exonerate/exonerate-2.4.0/codegen] ** (process:666679): WARNING **: 22:59:18.083: Creating codegen directory [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9] ** (process:666679): WARNING **: 22:59:18.083: Creating codegen directory [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9] ** Message: 22:59:18.084: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2dna_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2dna_32_find_32_score.c ** Message: 22:59:18.293: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2dna_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2dna_32_find_32_path.c ** Message: 22:59:18.556: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2dna_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2dna_32_find_32_region.c ** Message: 22:59:18.838: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.c ** Message: 22:59:19.556: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 22:59:20.434: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2dna_32_find_32_score.o] ** Message: 22:59:20.434: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2dna_32_find_32_score.o] to archive ar -cSq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2dna_32_find_32_score.o ** Message: 22:59:20.440: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_score] ** Message: 22:59:20.441: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2dna_32_find_32_path.o] ** Message: 22:59:20.441: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2dna_32_find_32_path.o ** Message: 22:59:20.446: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_path] ** Message: 22:59:20.446: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2dna_32_find_32_region.o] ** Message: 22:59:20.446: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2dna_32_find_32_region.o ** Message: 22:59:20.452: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_region] ** Message: 22:59:20.452: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.o] ** Message: 22:59:20.452: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.o ** Message: 22:59:20.457: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint] ** Message: 22:59:20.457: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 22:59:20.457: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 22:59:20.463: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation] ** Message: 22:59:20.463: Bootstrapper processing model [ungapped:protein2protein] ** Message: 22:59:20.463: Process optimal [optimal:ungapped:protein2protein] ** Message: 22:59:20.464: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2protein_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2protein_32_find_32_score.c ** Message: 22:59:20.890: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2protein_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2protein_32_find_32_path.c ** Message: 22:59:21.284: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2protein_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2protein_32_find_32_region.c ** Message: 22:59:21.558: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.c ** Message: 22:59:21.922: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.c ** Message: 22:59:22.570: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2protein_32_find_32_score.o] ** Message: 22:59:22.571: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2protein_32_find_32_score.o ** Message: 22:59:22.587: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_score] ** Message: 22:59:22.587: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2protein_32_find_32_path.o] ** Message: 22:59:22.587: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2protein_32_find_32_path.o ** Message: 22:59:22.593: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_path] ** Message: 22:59:22.593: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2protein_32_find_32_region.o] ** Message: 22:59:22.593: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2protein_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2protein_32_find_32_region.o ** Message: 22:59:22.598: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_region] ** Message: 22:59:22.598: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.o] ** Message: 22:59:22.599: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.o ** Message: 22:59:22.604: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint] ** Message: 22:59:22.604: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.o] ** Message: 22:59:22.604: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.o ** Message: 22:59:22.609: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation] ** Message: 22:59:22.610: Bootstrapper processing model [ungapped:dna2protein] ** Message: 22:59:22.610: Process optimal [optimal:ungapped:dna2protein] ** Message: 22:59:22.611: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2protein_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2protein_32_find_32_score.c ** Message: 22:59:22.900: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2protein_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2protein_32_find_32_path.c ** Message: 22:59:23.251: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2protein_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2protein_32_find_32_region.c ** Message: 22:59:23.646: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.c ** Message: 22:59:24.118: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.c ** Message: 22:59:24.621: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2protein_32_find_32_score.o] ** Message: 22:59:24.621: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2protein_32_find_32_score.o ** Message: 22:59:24.627: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_score] ** Message: 22:59:24.627: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2protein_32_find_32_path.o] ** Message: 22:59:24.627: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2protein_32_find_32_path.o ** Message: 22:59:24.633: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_path] ** Message: 22:59:24.633: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2protein_32_find_32_region.o] ** Message: 22:59:24.633: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2protein_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2protein_32_find_32_region.o ** Message: 22:59:24.638: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_region] ** Message: 22:59:24.639: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.o] ** Message: 22:59:24.639: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.o ** Message: 22:59:24.644: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint] ** Message: 22:59:24.644: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.o] ** Message: 22:59:24.644: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.o ** Message: 22:59:24.650: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation] ** Message: 22:59:24.650: Bootstrapper processing model [ungapped:protein2dna] ** Message: 22:59:24.650: Process optimal [optimal:ungapped:protein2dna] ** Message: 22:59:24.651: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2dna_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2dna_32_find_32_score.c ** Message: 22:59:24.929: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2dna_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2dna_32_find_32_path.c ** Message: 22:59:25.588: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2dna_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2dna_32_find_32_region.c ** Message: 22:59:26.291: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.c ** Message: 22:59:27.657: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.c ** Message: 22:59:28.858: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2dna_32_find_32_score.o] ** Message: 22:59:28.858: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2dna_32_find_32_score.o ** Message: 22:59:28.865: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_score] ** Message: 22:59:28.865: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2dna_32_find_32_path.o] ** Message: 22:59:28.865: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2dna_32_find_32_path.o ** Message: 22:59:28.871: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_path] ** Message: 22:59:28.871: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2dna_32_find_32_region.o] ** Message: 22:59:28.871: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2dna_32_find_32_region.o ** Message: 22:59:28.876: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_region] ** Message: 22:59:28.877: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.o] ** Message: 22:59:28.877: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.o ** Message: 22:59:28.882: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint] ** Message: 22:59:28.882: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.o] ** Message: 22:59:28.882: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.o ** Message: 22:59:28.888: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation] ** Message: 22:59:28.888: Processing model [u:t] ** Message: 22:59:28.889: Bootstrapper processing model [ungapped:codon] ** Message: 22:59:28.889: Process optimal [optimal:ungapped:codon] ** Message: 22:59:28.890: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_codon_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_codon_32_find_32_score.c ** Message: 22:59:29.610: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_codon_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_codon_32_find_32_path.c ** Message: 22:59:30.716: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_codon_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_codon_32_find_32_region.c ** Message: 22:59:32.720: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_codon_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_codon_32_find_32_checkpoint.c ** Message: 22:59:34.526: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.c ** Message: 22:59:35.981: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_codon_32_find_32_score.o] ** Message: 22:59:35.981: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_codon_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_codon_32_find_32_score.o ** Message: 22:59:35.988: Adding function [optimal_58_ungapped_58_codon_32_find_32_score] ** Message: 22:59:35.988: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_codon_32_find_32_path.o] ** Message: 22:59:35.988: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_codon_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_codon_32_find_32_path.o ** Message: 22:59:35.994: Adding function [optimal_58_ungapped_58_codon_32_find_32_path] ** Message: 22:59:35.994: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_codon_32_find_32_region.o] ** Message: 22:59:35.995: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_codon_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_codon_32_find_32_region.o ** Message: 22:59:36.001: Adding function [optimal_58_ungapped_58_codon_32_find_32_region] ** Message: 22:59:36.001: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_codon_32_find_32_checkpoint.o] ** Message: 22:59:36.001: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_codon_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_codon_32_find_32_checkpoint.o ** Message: 22:59:36.008: Adding function [optimal_58_ungapped_58_codon_32_find_32_checkpoint] ** Message: 22:59:36.008: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.o] ** Message: 22:59:36.008: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.o ** Message: 22:59:36.014: Adding function [optimal_58_ungapped_58_codon_32_find_32_path_32_continuation] ** Message: 22:59:36.015: Processing model [a:g] ** Message: 22:59:36.015: Bootstrapper processing model [affine:global:dna2dna] ** Message: 22:59:36.015: Process optimal [optimal:affine:global:dna2dna] ** Message: 22:59:36.016: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.c ** Message: 22:59:36.894: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.c ** Message: 22:59:38.951: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.c ** Message: 22:59:40.696: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 22:59:42.270: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.o] ** Message: 22:59:42.270: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.o ** Message: 22:59:42.277: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_score] ** Message: 22:59:42.277: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.o] ** Message: 22:59:42.277: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.o ** Message: 22:59:42.284: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_path] ** Message: 22:59:42.284: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.o] ** Message: 22:59:42.284: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.o ** Message: 22:59:42.291: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint] ** Message: 22:59:42.291: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 22:59:42.291: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 22:59:42.297: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation] ** Message: 22:59:42.298: Bootstrapper processing model [affine:global:protein2protein] ** Message: 22:59:42.298: Process optimal [optimal:affine:global:protein2protein] ** Message: 22:59:42.299: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.c ** Message: 22:59:43.439: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.c ** Message: 22:59:44.850: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.c ** Message: 22:59:46.666: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.c ** Message: 22:59:47.545: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.o] ** Message: 22:59:47.546: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.o ** Message: 22:59:47.552: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_score] ** Message: 22:59:47.552: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.o] ** Message: 22:59:47.553: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.o ** Message: 22:59:47.559: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_path] ** Message: 22:59:47.559: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.o] ** Message: 22:59:47.559: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.o ** Message: 22:59:47.566: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint] ** Message: 22:59:47.566: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.o] ** Message: 22:59:47.566: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.o ** Message: 22:59:47.574: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation] ** Message: 22:59:47.574: Processing model [a:b] ** Message: 22:59:47.575: Bootstrapper processing model [affine:bestfit:dna2dna] ** Message: 22:59:47.575: Process optimal [optimal:affine:bestfit:dna2dna] ** Message: 22:59:47.577: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.c ** Message: 22:59:48.335: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.c ** Message: 22:59:50.859: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.c ** Message: 22:59:52.408: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.c ** Message: 22:59:53.412: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 22:59:54.317: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.o] ** Message: 22:59:54.317: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.o ** Message: 22:59:54.324: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score] ** Message: 22:59:54.324: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.o] ** Message: 22:59:54.325: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.o ** Message: 22:59:54.331: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path] ** Message: 22:59:54.331: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.o] ** Message: 22:59:54.331: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.o ** Message: 22:59:54.338: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region] ** Message: 22:59:54.338: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.o] ** Message: 22:59:54.339: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.o ** Message: 22:59:54.345: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint] ** Message: 22:59:54.345: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 22:59:54.346: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 22:59:54.353: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation] ** Message: 22:59:54.354: Bootstrapper processing model [affine:bestfit:protein2protein] ** Message: 22:59:54.354: Process optimal [optimal:affine:bestfit:protein2protein] ** Message: 22:59:54.355: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.c ** Message: 22:59:56.519: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.c ** Message: 22:59:59.391: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.c ** Message: 23:00:00.664: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.c ** Message: 23:00:02.203: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.c ** Message: 23:00:03.914: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.o] ** Message: 23:00:03.914: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.o ** Message: 23:00:03.921: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score] ** Message: 23:00:03.921: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.o] ** Message: 23:00:03.921: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.o ** Message: 23:00:03.928: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path] ** Message: 23:00:03.928: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.o] ** Message: 23:00:03.928: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.o ** Message: 23:00:03.935: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region] ** Message: 23:00:03.936: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.o] ** Message: 23:00:03.936: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.o ** Message: 23:00:03.943: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint] ** Message: 23:00:03.943: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.o] ** Message: 23:00:03.943: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.o ** Message: 23:00:03.951: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation] ** Message: 23:00:03.951: Processing model [a:l] ** Message: 23:00:03.952: Bootstrapper processing model [affine:local:dna2dna] ** Message: 23:00:03.952: Process optimal [optimal:affine:local:dna2dna] ** Message: 23:00:03.952: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.c ** Message: 23:00:04.309: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.c ** Message: 23:00:05.160: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.c ** Message: 23:00:06.242: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.c ** Message: 23:00:07.670: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 23:00:09.194: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.o] ** Message: 23:00:09.194: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.o ** Message: 23:00:09.201: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_score] ** Message: 23:00:09.202: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.o] ** Message: 23:00:09.202: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.o ** Message: 23:00:09.209: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_path] ** Message: 23:00:09.209: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.o] ** Message: 23:00:09.209: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.o ** Message: 23:00:09.216: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_region] ** Message: 23:00:09.216: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o] ** Message: 23:00:09.217: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o ** Message: 23:00:09.224: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint] ** Message: 23:00:09.224: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 23:00:09.224: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 23:00:09.232: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation] ** Message: 23:00:09.235: Process optimal [Terminal [Segment("START"->"match"):[affine:local:dna2dna]]] ** Message: 23:00:09.237: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.c ** Message: 23:00:10.169: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.c ** Message: 23:00:11.649: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] ** Message: 23:00:11.649: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o ** Message: 23:00:11.657: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score] ** Message: 23:00:11.657: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 23:00:11.657: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 23:00:11.675: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path] ** Message: 23:00:11.675: Process optimal [Terminal [Segment("match"->"END"):[affine:local:dna2dna]]] ** Message: 23:00:11.677: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.c ** Message: 23:00:12.217: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.c ** Message: 23:00:13.107: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] ** Message: 23:00:13.108: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o ** Message: 23:00:13.116: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score] ** Message: 23:00:13.116: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 23:00:13.116: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 23:00:13.123: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path] ** Message: 23:00:13.123: Process optimal [HeuristicJoin:[Segment("match"->"match"):[affine:local:dna2dna]]] ** Message: 23:00:13.126: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.c ** Message: 23:00:15.634: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.c ** Message: 23:00:19.433: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] ** Message: 23:00:19.437: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o ** Message: 23:00:19.446: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score] ** Message: 23:00:19.446: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 23:00:19.446: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 23:00:19.454: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path] ** Message: 23:00:19.455: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.c ** Message: 23:00:19.953: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.c ** Message: 23:00:20.434: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.o] ** Message: 23:00:20.434: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.o ** Message: 23:00:20.453: Adding function [Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded] ** Message: 23:00:20.453: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.o] ** Message: 23:00:20.453: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.o ** Message: 23:00:20.461: Adding function [Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded] ** Message: 23:00:20.461: Bootstrapper processing model [affine:local:protein2protein] ** Message: 23:00:20.461: Process optimal [optimal:affine:local:protein2protein] ** Message: 23:00:20.462: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.c ** Message: 23:00:20.836: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.c ** Message: 23:00:21.538: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.c ** Message: 23:00:22.416: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.c ** Message: 23:00:23.774: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.c ** Message: 23:00:24.734: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.o] ** Message: 23:00:24.735: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.o ** Message: 23:00:24.744: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_score] ** Message: 23:00:24.745: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.o] ** Message: 23:00:24.745: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.o ** Message: 23:00:24.752: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_path] ** Message: 23:00:24.753: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.o] ** Message: 23:00:24.753: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.o ** Message: 23:00:24.761: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_region] ** Message: 23:00:24.761: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o] ** Message: 23:00:24.761: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o ** Message: 23:00:24.769: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint] ** Message: 23:00:24.790: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o] ** Message: 23:00:24.790: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o ** Message: 23:00:24.798: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation] ** Message: 23:00:24.801: Process optimal [Terminal [Segment("START"->"match"):[affine:local:protein2protein]]] ** Message: 23:00:24.803: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.c ** Message: 23:00:26.702: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.c ** Message: 23:00:29.394: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] ** Message: 23:00:29.394: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o ** Message: 23:00:29.402: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score] ** Message: 23:00:29.403: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 23:00:29.403: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 23:00:29.412: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path] ** Message: 23:00:29.412: Process optimal [Terminal [Segment("match"->"END"):[affine:local:protein2protein]]] ** Message: 23:00:29.413: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.c ** Message: 23:00:31.160: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.c ** Message: 23:00:32.753: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] ** Message: 23:00:32.753: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o ** Message: 23:00:32.762: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score] ** Message: 23:00:32.762: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 23:00:32.762: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 23:00:32.770: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path] ** Message: 23:00:32.770: Process optimal [HeuristicJoin:[Segment("match"->"match"):[affine:local:protein2protein]]] ** Message: 23:00:32.773: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.c ** Message: 23:00:34.817: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.c ** Message: 23:00:39.028: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] ** Message: 23:00:39.028: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o ** Message: 23:00:39.037: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score] ** Message: 23:00:39.037: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 23:00:39.037: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 23:00:39.045: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path] ** Message: 23:00:39.046: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.c ** Message: 23:00:39.418: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.c ** Message: 23:00:39.847: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.o] ** Message: 23:00:39.847: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.o ** Message: 23:00:39.856: Adding function [Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded] ** Message: 23:00:39.856: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.o] ** Message: 23:00:39.856: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.o ** Message: 23:00:39.864: Adding function [Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded] ** Message: 23:00:39.865: Processing model [a:o] ** Message: 23:00:39.865: Bootstrapper processing model [affine:overlap:dna2dna] ** Message: 23:00:39.865: Process optimal [optimal:affine:overlap:dna2dna] ** Message: 23:00:39.867: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.c ** Message: 23:00:41.610: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.c ** Message: 23:00:44.024: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.c ** Message: 23:00:45.410: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.c ** Message: 23:00:46.505: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 23:00:47.851: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.o] ** Message: 23:00:47.851: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.o ** Message: 23:00:47.860: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score] ** Message: 23:00:47.860: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.o] ** Message: 23:00:47.860: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.o ** Message: 23:00:47.869: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path] ** Message: 23:00:47.869: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.o] ** Message: 23:00:47.869: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.o ** Message: 23:00:47.879: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region] ** Message: 23:00:47.880: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.o] ** Message: 23:00:47.880: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.o ** Message: 23:00:47.890: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint] ** Message: 23:00:47.890: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 23:00:47.891: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 23:00:47.901: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation] ** Message: 23:00:47.901: Processing model [e2g] ** Message: 23:00:47.902: Bootstrapper processing model [est2genome] ** Message: 23:00:47.902: Process optimal [optimal:est2genome] ** Message: 23:00:47.904: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_est2genome_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_est2genome_32_find_32_score.c ** Message: 23:00:49.342: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_est2genome_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_est2genome_32_find_32_path.c ** Message: 23:00:51.762: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_est2genome_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_est2genome_32_find_32_region.c ** Message: 23:00:53.873: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_est2genome_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_est2genome_32_find_32_checkpoint.c ** Message: 23:00:59.481: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_est2genome_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_est2genome_32_find_32_path_32_continuation.c ** Message: 23:01:07.223: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_est2genome_32_find_32_score.o] ** Message: 23:01:07.223: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_est2genome_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_est2genome_32_find_32_score.o ** Message: 23:01:07.233: Adding function [optimal_58_est2genome_32_find_32_score] ** Message: 23:01:07.233: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_est2genome_32_find_32_path.o] ** Message: 23:01:07.233: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_est2genome_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_est2genome_32_find_32_path.o ** Message: 23:01:07.242: Adding function [optimal_58_est2genome_32_find_32_path] ** Message: 23:01:07.242: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_est2genome_32_find_32_region.o] ** Message: 23:01:07.242: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_est2genome_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_est2genome_32_find_32_region.o ** Message: 23:01:07.252: Adding function [optimal_58_est2genome_32_find_32_region] ** Message: 23:01:07.252: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_est2genome_32_find_32_checkpoint.o] ** Message: 23:01:07.252: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_est2genome_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_est2genome_32_find_32_checkpoint.o ** Message: 23:01:07.261: Adding function [optimal_58_est2genome_32_find_32_checkpoint] ** Message: 23:01:07.261: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_est2genome_32_find_32_path_32_continuation.o] ** Message: 23:01:07.262: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_est2genome_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_est2genome_32_find_32_path_32_continuation.o ** Message: 23:01:07.271: Adding function [optimal_58_est2genome_32_find_32_path_32_continuation] ** Message: 23:01:07.282: Process optimal [Terminal [Segment("START"->"match reverse"):[est2genome]]] ** Message: 23:01:07.285: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 23:01:09.459: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 23:01:14.041: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 23:01:14.041: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 23:01:14.051: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score] ** Message: 23:01:14.052: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 23:01:14.052: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 23:01:14.061: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 23:01:14.061: Process optimal [Terminal [Segment("match reverse"->"END"):[est2genome]]] ** Message: 23:01:14.064: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 23:01:15.347: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 23:01:17.424: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 23:01:17.424: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 23:01:17.434: Adding function [Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score] ** Message: 23:01:17.434: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 23:01:17.434: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 23:01:17.445: Adding function [Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 23:01:17.445: Process optimal [Terminal [Segment("START"->"match forward"):[est2genome]]] ** Message: 23:01:17.448: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 23:01:19.992: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 23:01:23.001: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 23:01:23.003: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 23:01:23.012: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score] ** Message: 23:01:23.012: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 23:01:23.012: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 23:01:23.022: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 23:01:23.022: Process optimal [Terminal [Segment("match forward"->"END"):[est2genome]]] ** Message: 23:01:23.024: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 23:01:24.054: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 23:01:25.655: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 23:01:25.656: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 23:01:25.668: Adding function [Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score] ** Message: 23:01:25.668: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 23:01:25.668: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 23:01:25.688: Adding function [Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 23:01:25.688: Process optimal [HeuristicJoin:[Segment("match reverse"->"match reverse"):[est2genome]]] ** Message: 23:01:25.703: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 23:01:29.793: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 23:01:37.327: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 23:01:37.328: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 23:01:37.339: Adding function [HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score] ** Message: 23:01:37.340: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 23:01:37.340: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 23:01:37.349: Adding function [HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 23:01:37.350: Process optimal [Src span [Segment("match reverse"->"intron reverse"):[est2genome]]] ** Message: 23:01:37.352: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 23:01:38.855: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 23:01:41.498: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 23:01:41.499: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 23:01:41.510: Adding function [Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score] ** Message: 23:01:41.510: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 23:01:41.510: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 23:01:41.520: Adding function [Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 23:01:41.520: Process optimal [Src span traceback [Segment("match reverse"->"intron reverse"):[est2genome]]] ** Message: 23:01:41.524: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 23:01:48.581: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 23:01:48.581: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 23:01:48.592: Adding function [Src_32_span_32_traceback_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 23:01:48.592: Process optimal [Dst span [Segment("intron reverse"->"match reverse"):[est2genome]]] ** Message: 23:01:48.595: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 23:01:50.538: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 23:01:54.645: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 23:01:54.645: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 23:01:54.656: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score] ** Message: 23:01:54.656: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 23:01:54.656: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 23:01:54.667: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 23:01:54.667: Process optimal [HeuristicJoin:[Segment("match forward"->"match forward"):[est2genome]]] ** Message: 23:01:54.673: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 23:02:02.456: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 23:02:10.313: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 23:02:10.314: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 23:02:10.325: Adding function [HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score] ** Message: 23:02:10.326: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 23:02:10.326: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 23:02:10.336: Adding function [HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 23:02:10.337: Process optimal [Src span [Segment("match forward"->"intron forward"):[est2genome]]] ** Message: 23:02:10.339: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 23:02:12.083: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 23:02:13.564: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 23:02:13.564: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 23:02:13.575: Adding function [Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score] ** Message: 23:02:13.575: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 23:02:13.575: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 23:02:13.587: Adding function [Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 23:02:13.587: Process optimal [Src span traceback [Segment("match forward"->"intron forward"):[est2genome]]] ** Message: 23:02:13.593: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 23:02:18.797: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 23:02:18.797: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 23:02:18.808: Adding function [Src_32_span_32_traceback_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 23:02:18.809: Process optimal [Dst span [Segment("intron forward"->"match forward"):[est2genome]]] ** Message: 23:02:18.820: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 23:02:20.750: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 23:02:24.038: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 23:02:24.038: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 23:02:24.050: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score] ** Message: 23:02:24.050: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 23:02:24.050: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 23:02:24.061: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 23:02:24.062: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.c ** Message: 23:02:24.624: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.c ** Message: 23:02:25.836: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.o] ** Message: 23:02:25.837: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.o ** Message: 23:02:25.848: Adding function [Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary] ** Message: 23:02:25.848: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.o] ** Message: 23:02:25.848: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.o ** Message: 23:02:25.860: Adding function [Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary] ** Message: 23:02:25.861: Processing model [ner] ** Message: 23:02:25.861: Bootstrapper processing model [NER:affine:local:dna2dna] ** Message: 23:02:25.861: Process optimal [optimal:NER:affine:local:dna2dna] ** Message: 23:02:25.862: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.c ** Message: 23:02:26.225: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.c ** Message: 23:02:26.769: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.c ** Message: 23:02:27.262: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.c ** Message: 23:02:28.362: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 23:02:29.860: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.o] ** Message: 23:02:29.861: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.o ** Message: 23:02:29.872: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score] ** Message: 23:02:29.872: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.o] ** Message: 23:02:29.872: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.o ** Message: 23:02:29.883: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path] ** Message: 23:02:29.884: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.o] ** Message: 23:02:29.884: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.o ** Message: 23:02:29.895: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region] ** Message: 23:02:29.895: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o] ** Message: 23:02:29.895: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o ** Message: 23:02:29.906: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint] ** Message: 23:02:29.907: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 23:02:29.907: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 23:02:29.919: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation] ** Message: 23:02:29.925: Process optimal [Terminal [Segment("START"->"match"):[NER:affine:local:dna2dna]]] ** Message: 23:02:29.927: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.c ** Message: 23:02:31.598: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.c ** Message: 23:02:34.260: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] ** Message: 23:02:34.261: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o ** Message: 23:02:34.273: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score] ** Message: 23:02:34.273: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 23:02:34.273: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 23:02:34.285: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path] ** Message: 23:02:34.285: Process optimal [Terminal [Segment("match"->"END"):[NER:affine:local:dna2dna]]] ** Message: 23:02:34.286: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.c ** Message: 23:02:35.452: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.c ** Message: 23:02:37.757: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] ** Message: 23:02:37.757: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o ** Message: 23:02:37.779: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score] ** Message: 23:02:37.780: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 23:02:37.780: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 23:02:37.792: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path] ** Message: 23:02:37.792: Process optimal [HeuristicJoin:[Segment("match"->"match"):[NER:affine:local:dna2dna]]] ** Message: 23:02:37.796: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.c ** Message: 23:02:41.616: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.c ** Message: 23:02:46.367: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] ** Message: 23:02:46.368: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o ** Message: 23:02:46.381: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score] ** Message: 23:02:46.381: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 23:02:46.381: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 23:02:46.393: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path] ** Message: 23:02:46.393: Process optimal [Src span [Segment("match"->"ner"):[NER:affine:local:dna2dna]]] ** Message: 23:02:46.394: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.c ** Message: 23:02:47.096: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.c ** Message: 23:02:48.222: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] ** Message: 23:02:48.222: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o ** Message: 23:02:48.234: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score] ** Message: 23:02:48.234: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 23:02:48.234: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 23:02:48.246: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path] ** Message: 23:02:48.246: Process optimal [Src span traceback [Segment("match"->"ner"):[NER:affine:local:dna2dna]]] ** Message: 23:02:48.250: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.c ** Message: 23:02:51.987: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 23:02:51.987: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 23:02:51.999: Adding function [Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path] ** Message: 23:02:51.999: Process optimal [Dst span [Segment("ner"->"match"):[NER:affine:local:dna2dna]]] ** Message: 23:02:52.001: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.c ** Message: 23:02:53.428: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.c ** Message: 23:02:55.849: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] ** Message: 23:02:55.849: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o ** Message: 23:02:55.861: Adding function [Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score] ** Message: 23:02:55.861: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 23:02:55.861: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 23:02:55.873: Adding function [Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path] ** Message: 23:02:55.875: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.c ** Message: 23:02:56.212: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.c ** Message: 23:02:56.608: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.o] ** Message: 23:02:56.608: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.o ** Message: 23:02:56.621: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary] ** Message: 23:02:56.621: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.o] ** Message: 23:02:56.621: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.o ** Message: 23:02:56.635: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary] ** Message: 23:02:56.636: Bootstrapper processing model [NER:affine:local:protein2protein] ** Message: 23:02:56.636: Process optimal [optimal:NER:affine:local:protein2protein] ** Message: 23:02:56.637: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.c ** Message: 23:02:57.090: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.c ** Message: 23:02:57.654: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.c ** Message: 23:02:58.356: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.c ** Message: 23:02:59.723: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.c ** Message: 23:03:01.047: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.o] ** Message: 23:03:01.048: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.o ** Message: 23:03:01.070: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score] ** Message: 23:03:01.070: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.o] ** Message: 23:03:01.070: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.o ** Message: 23:03:01.082: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path] ** Message: 23:03:01.083: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.o] ** Message: 23:03:01.083: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.o ** Message: 23:03:01.094: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region] ** Message: 23:03:01.095: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o] ** Message: 23:03:01.095: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o ** Message: 23:03:01.107: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint] ** Message: 23:03:01.108: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o] ** Message: 23:03:01.108: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o ** Message: 23:03:01.120: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation] ** Message: 23:03:01.125: Process optimal [Terminal [Segment("START"->"match"):[NER:affine:local:protein2protein]]] ** Message: 23:03:01.127: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.c ** Message: 23:03:02.084: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.c ** Message: 23:03:03.541: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] ** Message: 23:03:03.541: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o ** Message: 23:03:03.550: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score] ** Message: 23:03:03.551: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 23:03:03.551: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 23:03:03.561: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path] ** Message: 23:03:03.561: Process optimal [Terminal [Segment("match"->"END"):[NER:affine:local:protein2protein]]] ** Message: 23:03:03.562: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.c ** Message: 23:03:04.291: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.c ** Message: 23:03:06.130: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] ** Message: 23:03:06.131: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o ** Message: 23:03:06.143: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score] ** Message: 23:03:06.143: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 23:03:06.143: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 23:03:06.156: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path] ** Message: 23:03:06.156: Process optimal [HeuristicJoin:[Segment("match"->"match"):[NER:affine:local:protein2protein]]] ** Message: 23:03:06.160: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.c ** Message: 23:03:08.569: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.c ** Message: 23:03:14.065: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] ** Message: 23:03:14.066: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o ** Message: 23:03:14.079: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score] ** Message: 23:03:14.080: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 23:03:14.080: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 23:03:14.093: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path] ** Message: 23:03:14.093: Process optimal [Src span [Segment("match"->"ner"):[NER:affine:local:protein2protein]]] ** Message: 23:03:14.095: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.c ** Message: 23:03:14.845: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.c ** Message: 23:03:16.229: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] ** Message: 23:03:16.230: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o ** Message: 23:03:16.241: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score] ** Message: 23:03:16.242: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 23:03:16.242: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 23:03:16.255: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path] ** Message: 23:03:16.255: Process optimal [Src span traceback [Segment("match"->"ner"):[NER:affine:local:protein2protein]]] ** Message: 23:03:16.260: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.c ** Message: 23:03:21.804: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 23:03:21.804: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 23:03:21.817: Adding function [Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path] ** Message: 23:03:21.817: Process optimal [Dst span [Segment("ner"->"match"):[NER:affine:local:protein2protein]]] ** Message: 23:03:21.820: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.c ** Message: 23:03:24.374: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.c ** Message: 23:03:26.995: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] ** Message: 23:03:26.995: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o ** Message: 23:03:27.008: Adding function [Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score] ** Message: 23:03:27.009: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 23:03:27.009: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 23:03:27.023: Adding function [Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path] ** Message: 23:03:27.024: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.c ** Message: 23:03:27.928: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.c ** Message: 23:03:28.705: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.o] ** Message: 23:03:28.706: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.o ** Message: 23:03:28.719: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary] ** Message: 23:03:28.720: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.o] ** Message: 23:03:28.720: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.o ** Message: 23:03:28.733: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary] ** Message: 23:03:28.733: Processing model [p2d] ** Message: 23:03:28.734: Bootstrapper processing model [protein2dna:local] ** Message: 23:03:28.734: Process optimal [optimal:protein2dna:local] ** Message: 23:03:28.736: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_local_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_local_32_find_32_score.c ** Message: 23:03:29.681: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_local_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_local_32_find_32_path.c ** Message: 23:03:30.974: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_local_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_local_32_find_32_region.c ** Message: 23:03:33.681: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_local_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_local_32_find_32_checkpoint.c ** Message: 23:03:38.600: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.c ** Message: 23:03:43.563: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_local_32_find_32_score.o] ** Message: 23:03:43.563: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_local_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_local_32_find_32_score.o ** Message: 23:03:43.577: Adding function [optimal_58_protein2dna_58_local_32_find_32_score] ** Message: 23:03:43.577: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_local_32_find_32_path.o] ** Message: 23:03:43.577: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_local_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_local_32_find_32_path.o ** Message: 23:03:43.591: Adding function [optimal_58_protein2dna_58_local_32_find_32_path] ** Message: 23:03:43.591: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_local_32_find_32_region.o] ** Message: 23:03:43.591: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_local_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_local_32_find_32_region.o ** Message: 23:03:43.606: Adding function [optimal_58_protein2dna_58_local_32_find_32_region] ** Message: 23:03:43.607: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_local_32_find_32_checkpoint.o] ** Message: 23:03:43.607: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_local_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_local_32_find_32_checkpoint.o ** Message: 23:03:43.631: Adding function [optimal_58_protein2dna_58_local_32_find_32_checkpoint] ** Message: 23:03:43.631: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.o] ** Message: 23:03:43.631: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.o ** Message: 23:03:43.651: Adding function [optimal_58_protein2dna_58_local_32_find_32_path_32_continuation] ** Message: 23:03:43.661: Process optimal [Terminal [Segment("START"->"match"):[protein2dna:local]]] ** Message: 23:03:43.665: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.c ** Message: 23:03:49.711: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.c ** Message: 23:03:53.726: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] ** Message: 23:03:53.726: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o ** Message: 23:03:53.741: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score] ** Message: 23:03:53.741: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] ** Message: 23:03:53.741: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o ** Message: 23:03:53.756: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path] ** Message: 23:03:53.756: Process optimal [Terminal [Segment("match"->"END"):[protein2dna:local]]] ** Message: 23:03:53.758: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.c ** Message: 23:03:55.686: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.c ** Message: 23:03:57.771: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] ** Message: 23:03:57.771: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o ** Message: 23:03:57.785: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score] ** Message: 23:03:57.785: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] ** Message: 23:03:57.785: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o ** Message: 23:03:57.800: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path] ** Message: 23:03:57.800: Process optimal [HeuristicJoin:[Segment("match"->"match"):[protein2dna:local]]] ** Message: 23:03:57.806: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.c ** Message: 23:04:03.652: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.c ** Message: 23:04:12.210: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] ** Message: 23:04:12.212: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o ** Message: 23:04:12.235: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score] ** Message: 23:04:12.235: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] ** Message: 23:04:12.235: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o ** Message: 23:04:12.259: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path] ** Message: 23:04:12.260: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.c ** Message: 23:04:12.847: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.c ** Message: 23:04:13.203: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.o] ** Message: 23:04:13.203: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.o ** Message: 23:04:13.218: Adding function [Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded] ** Message: 23:04:13.218: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.o] ** Message: 23:04:13.218: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.o ** Message: 23:04:13.231: Adding function [Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded] ** Message: 23:04:13.232: Processing model [p2d:b] ** Message: 23:04:13.232: Bootstrapper processing model [protein2dna:bestfit] ** Message: 23:04:13.232: Process optimal [optimal:protein2dna:bestfit] ** Message: 23:04:13.236: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_bestfit_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_bestfit_32_find_32_score.c ** Message: 23:04:15.751: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_bestfit_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_bestfit_32_find_32_path.c ** Message: 23:04:20.685: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_bestfit_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_bestfit_32_find_32_region.c ** Message: 23:04:23.821: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.c ** Message: 23:04:25.857: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.c ** Message: 23:04:28.623: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_bestfit_32_find_32_score.o] ** Message: 23:04:28.649: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_bestfit_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_bestfit_32_find_32_score.o ** Message: 23:04:28.664: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_score] ** Message: 23:04:28.664: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_bestfit_32_find_32_path.o] ** Message: 23:04:28.664: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_bestfit_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_bestfit_32_find_32_path.o ** Message: 23:04:28.679: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_path] ** Message: 23:04:28.679: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_bestfit_32_find_32_region.o] ** Message: 23:04:28.679: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_bestfit_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_bestfit_32_find_32_region.o ** Message: 23:04:28.693: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_region] ** Message: 23:04:28.693: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.o] ** Message: 23:04:28.693: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.o ** Message: 23:04:28.707: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint] ** Message: 23:04:28.707: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.o] ** Message: 23:04:28.707: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.o ** Message: 23:04:28.722: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation] ** Message: 23:04:28.722: Processing model [p2g] ** Message: 23:04:28.723: Bootstrapper processing model [protein2genome:local] ** Message: 23:04:28.723: Process optimal [optimal:protein2genome:local] ** Message: 23:04:28.726: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_local_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_local_32_find_32_score.c ** Message: 23:04:30.327: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_local_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_local_32_find_32_path.c ** Message: 23:04:32.729: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_local_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_local_32_find_32_region.c ** Message: 23:04:35.625: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_local_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_local_32_find_32_checkpoint.c ** Message: 23:04:46.469: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.c ** Message: 23:04:55.833: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_local_32_find_32_score.o] ** Message: 23:04:55.833: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_local_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_local_32_find_32_score.o ** Message: 23:04:55.848: Adding function [optimal_58_protein2genome_58_local_32_find_32_score] ** Message: 23:04:55.848: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_local_32_find_32_path.o] ** Message: 23:04:55.848: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_local_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_local_32_find_32_path.o ** Message: 23:04:55.863: Adding function [optimal_58_protein2genome_58_local_32_find_32_path] ** Message: 23:04:55.863: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_local_32_find_32_region.o] ** Message: 23:04:55.863: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_local_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_local_32_find_32_region.o ** Message: 23:04:55.877: Adding function [optimal_58_protein2genome_58_local_32_find_32_region] ** Message: 23:04:55.879: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_local_32_find_32_checkpoint.o] ** Message: 23:04:55.879: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_local_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_local_32_find_32_checkpoint.o ** Message: 23:04:55.894: Adding function [optimal_58_protein2genome_58_local_32_find_32_checkpoint] ** Message: 23:04:55.894: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.o] ** Message: 23:04:55.895: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.o ** Message: 23:04:55.909: Adding function [optimal_58_protein2genome_58_local_32_find_32_path_32_continuation] ** Message: 23:04:55.950: Process optimal [Terminal [Segment("START"->"match"):[protein2genome:local]]] ** Message: 23:04:55.958: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 23:05:03.539: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 23:05:21.221: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 23:05:21.222: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 23:05:21.238: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score] ** Message: 23:05:21.238: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 23:05:21.238: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 23:05:21.254: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] ** Message: 23:05:21.254: Process optimal [Terminal [Segment("match"->"END"):[protein2genome:local]]] ** Message: 23:05:21.259: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 23:05:28.256: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 23:05:37.639: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 23:05:37.640: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 23:05:37.655: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score] ** Message: 23:05:37.655: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 23:05:37.655: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 23:05:37.671: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] ** Message: 23:05:37.671: Process optimal [HeuristicJoin:[Segment("match"->"match"):[protein2genome:local]]] ** Message: 23:05:37.684: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 23:05:55.223: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 23:06:26.132: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 23:06:26.143: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 23:06:26.168: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score] ** Message: 23:06:26.168: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 23:06:26.168: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 23:06:26.185: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] ** Message: 23:06:26.185: Process optimal [Src span [Segment("match"->"intron 0:0 phase-T"):[protein2genome:local]]] ** Message: 23:06:26.190: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 23:06:30.182: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 23:06:36.492: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 23:06:36.493: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 23:06:36.534: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score] ** Message: 23:06:36.535: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 23:06:36.535: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 23:06:36.550: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] ** Message: 23:06:36.551: Process optimal [Src span traceback [Segment("match"->"intron 0:0 phase-T"):[protein2genome:local]]] ** Message: 23:06:36.565: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 23:07:17.613: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 23:07:17.616: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 23:07:17.634: Adding function [Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] ** Message: 23:07:17.634: Process optimal [Dst span [Segment("intron 0:0 phase-T"->"match"):[protein2genome:local]]] ** Message: 23:07:17.643: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 23:07:29.300: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 23:07:59.655: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 23:07:59.655: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 23:07:59.683: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score] ** Message: 23:07:59.683: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 23:07:59.683: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 23:07:59.702: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] ** Message: 23:07:59.702: Process optimal [Src span [Segment("match"->"intron 1:2 phase-T"):[protein2genome:local]]] ** Message: 23:07:59.707: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 23:08:03.914: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 23:08:09.521: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 23:08:09.521: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 23:08:09.539: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score] ** Message: 23:08:09.540: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 23:08:09.540: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 23:08:09.558: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] ** Message: 23:08:09.558: Process optimal [Src span traceback [Segment("match"->"intron 1:2 phase-T"):[protein2genome:local]]] ** Message: 23:08:09.572: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 23:08:37.150: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 23:08:37.150: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 23:08:37.168: Adding function [Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] ** Message: 23:08:37.168: Process optimal [Dst span [Segment("intron 1:2 phase-T"->"match"):[protein2genome:local]]] ** Message: 23:08:37.177: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 23:08:45.043: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 23:09:03.905: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 23:09:03.905: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 23:09:03.925: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score] ** Message: 23:09:03.925: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 23:09:03.926: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 23:09:03.947: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] ** Message: 23:09:03.947: Process optimal [Src span [Segment("match"->"intron 2:1 phase-T"):[protein2genome:local]]] ** Message: 23:09:03.952: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 23:09:09.063: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 23:09:15.311: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 23:09:15.311: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 23:09:15.330: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score] ** Message: 23:09:15.330: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 23:09:15.330: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 23:09:15.349: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] ** Message: 23:09:15.349: Process optimal [Src span traceback [Segment("match"->"intron 2:1 phase-T"):[protein2genome:local]]] ** Message: 23:09:15.384: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 23:09:56.417: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 23:09:56.417: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 23:09:56.436: Adding function [Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] ** Message: 23:09:56.436: Process optimal [Dst span [Segment("intron 2:1 phase-T"->"match"):[protein2genome:local]]] ** Message: 23:09:56.445: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 23:10:07.625: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 23:10:26.978: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 23:10:26.978: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 23:10:26.998: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score] ** Message: 23:10:26.998: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 23:10:26.998: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 23:10:27.019: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] ** Message: 23:10:27.022: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.c ** Message: 23:10:28.752: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.c ** Message: 23:10:30.270: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.o] ** Message: 23:10:30.270: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.o ** Message: 23:10:30.290: Adding function [Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary] ** Message: 23:10:30.290: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.o] ** Message: 23:10:30.290: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.o ** Message: 23:10:30.310: Adding function [Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary] ** Message: 23:10:30.310: Processing model [p2g:b] ** Message: 23:10:30.311: Bootstrapper processing model [protein2genome:bestfit] ** Message: 23:10:30.311: Process optimal [optimal:protein2genome:bestfit] ** Message: 23:10:30.321: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_bestfit_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_bestfit_32_find_32_score.c ** Message: 23:10:43.629: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_bestfit_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_bestfit_32_find_32_path.c ** Message: 23:10:59.780: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_bestfit_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_bestfit_32_find_32_region.c ** Message: 23:11:15.324: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.c ** Message: 23:11:25.850: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.c ** Message: 23:11:45.594: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_bestfit_32_find_32_score.o] ** Message: 23:11:45.595: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_bestfit_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_bestfit_32_find_32_score.o ** Message: 23:11:45.615: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_score] ** Message: 23:11:45.615: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_bestfit_32_find_32_path.o] ** Message: 23:11:45.615: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_bestfit_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_bestfit_32_find_32_path.o ** Message: 23:11:45.636: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_path] ** Message: 23:11:45.636: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_bestfit_32_find_32_region.o] ** Message: 23:11:45.636: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_bestfit_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_bestfit_32_find_32_region.o ** Message: 23:11:45.656: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_region] ** Message: 23:11:45.656: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.o] ** Message: 23:11:45.656: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.o ** Message: 23:11:45.676: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint] ** Message: 23:11:45.676: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.o] ** Message: 23:11:45.676: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.o ** Message: 23:11:45.717: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation] ** Message: 23:11:45.718: Processing model [c2c] ** Message: 23:11:45.719: Bootstrapper processing model [coding2coding] ** Message: 23:11:45.719: Process optimal [optimal:coding2coding] ** Message: 23:11:45.722: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2coding_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2coding_32_find_32_score.c ** Message: 23:11:48.724: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2coding_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2coding_32_find_32_path.c ** Message: 23:11:52.719: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2coding_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2coding_32_find_32_region.c ** Message: 23:11:56.077: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2coding_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2coding_32_find_32_checkpoint.c ** Message: 23:12:10.636: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2coding_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2coding_32_find_32_path_32_continuation.c ** Message: 23:12:29.224: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2coding_32_find_32_score.o] ** Message: 23:12:29.226: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2coding_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2coding_32_find_32_score.o ** Message: 23:12:29.248: Adding function [optimal_58_coding2coding_32_find_32_score] ** Message: 23:12:29.248: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2coding_32_find_32_path.o] ** Message: 23:12:29.248: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2coding_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2coding_32_find_32_path.o ** Message: 23:12:29.269: Adding function [optimal_58_coding2coding_32_find_32_path] ** Message: 23:12:29.269: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2coding_32_find_32_region.o] ** Message: 23:12:29.269: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2coding_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2coding_32_find_32_region.o ** Message: 23:12:29.291: Adding function [optimal_58_coding2coding_32_find_32_region] ** Message: 23:12:29.292: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2coding_32_find_32_checkpoint.o] ** Message: 23:12:29.292: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2coding_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2coding_32_find_32_checkpoint.o ** Message: 23:12:29.313: Adding function [optimal_58_coding2coding_32_find_32_checkpoint] ** Message: 23:12:29.313: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2coding_32_find_32_path_32_continuation.o] ** Message: 23:12:29.313: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2coding_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2coding_32_find_32_path_32_continuation.o ** Message: 23:12:29.334: Adding function [optimal_58_coding2coding_32_find_32_path_32_continuation] ** Message: 23:12:29.372: Process optimal [Terminal [Segment("START"->"match"):[coding2coding]]] ** Message: 23:12:29.380: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.c ** Message: 23:12:41.386: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.c ** Message: 23:12:58.857: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o] ** Message: 23:12:58.857: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o ** Message: 23:12:58.878: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score] ** Message: 23:12:58.878: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o] ** Message: 23:12:58.879: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o ** Message: 23:12:58.900: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path] ** Message: 23:12:58.901: Process optimal [Terminal [Segment("match"->"END"):[coding2coding]]] ** Message: 23:12:58.905: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_score.c ** Message: 23:13:01.360: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_path.c ** Message: 23:13:05.873: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_score.o] ** Message: 23:13:05.873: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_score.o ** Message: 23:13:05.894: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_score] ** Message: 23:13:05.895: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_path.o] ** Message: 23:13:05.895: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_path.o ** Message: 23:13:05.915: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_path] ** Message: 23:13:05.916: Process optimal [HeuristicJoin:[Segment("match"->"match"):[coding2coding]]] ** Message: 23:13:05.927: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.c ** Message: 23:13:25.124: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.c ** Message: 23:14:33.543: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o] ** Message: 23:14:33.543: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o ** Message: 23:14:33.565: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score] ** Message: 23:14:33.565: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o] ** Message: 23:14:33.565: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o ** Message: 23:14:33.597: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path] ** Message: 23:14:33.599: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.c ** Message: 23:14:34.438: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.c ** Message: 23:14:35.247: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.o] ** Message: 23:14:35.248: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.o ** Message: 23:14:35.270: Adding function [Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded] ** Message: 23:14:35.270: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.o] ** Message: 23:14:35.271: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.o ** Message: 23:14:35.300: Adding function [Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded] ** Message: 23:14:35.301: Processing model [c2g] ** Message: 23:14:35.302: Bootstrapper processing model [coding2genome] ** Message: 23:14:35.302: Process optimal [optimal:coding2genome] ** Message: 23:14:35.308: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2genome_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2genome_32_find_32_score.c ** Message: 23:14:41.850: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2genome_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2genome_32_find_32_path.c ** Message: 23:14:54.065: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2genome_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2genome_32_find_32_region.c ** Message: 23:15:02.343: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2genome_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2genome_32_find_32_checkpoint.c ** Message: 23:15:32.707: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2genome_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2genome_32_find_32_path_32_continuation.c ** Message: 23:16:25.145: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2genome_32_find_32_score.o] ** Message: 23:16:25.147: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2genome_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2genome_32_find_32_score.o ** Message: 23:16:25.190: Adding function [optimal_58_coding2genome_32_find_32_score] ** Message: 23:16:25.190: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2genome_32_find_32_path.o] ** Message: 23:16:25.190: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2genome_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2genome_32_find_32_path.o ** Message: 23:16:25.212: Adding function [optimal_58_coding2genome_32_find_32_path] ** Message: 23:16:25.212: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2genome_32_find_32_region.o] ** Message: 23:16:25.212: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2genome_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2genome_32_find_32_region.o ** Message: 23:16:25.234: Adding function [optimal_58_coding2genome_32_find_32_region] ** Message: 23:16:25.234: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2genome_32_find_32_checkpoint.o] ** Message: 23:16:25.234: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2genome_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2genome_32_find_32_checkpoint.o ** Message: 23:16:25.256: Adding function [optimal_58_coding2genome_32_find_32_checkpoint] ** Message: 23:16:25.256: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2genome_32_find_32_path_32_continuation.o] ** Message: 23:16:25.256: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2genome_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2genome_32_find_32_path_32_continuation.o ** Message: 23:16:25.280: Adding function [optimal_58_coding2genome_32_find_32_path_32_continuation] ** Message: 23:16:25.282: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.c ** Message: 23:16:26.487: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.c ** Message: 23:16:27.531: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.o] ** Message: 23:16:27.531: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.o ** Message: 23:16:27.553: Adding function [Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary] ** Message: 23:16:27.553: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.o] ** Message: 23:16:27.553: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.o ** Message: 23:16:27.575: Adding function [Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary] ** Message: 23:16:27.576: Processing model [cd2g] ** Message: 23:16:27.578: Bootstrapper processing model [cdna2genome] ** Message: 23:16:27.578: Process optimal [optimal:cdna2genome] ** Message: 23:16:27.590: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_cdna2genome_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_cdna2genome_32_find_32_score.c ** Message: 23:16:42.346: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_cdna2genome_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_cdna2genome_32_find_32_path.c ** Message: 23:17:06.715: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_cdna2genome_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_cdna2genome_32_find_32_region.c ** Message: 23:17:29.421: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_cdna2genome_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_cdna2genome_32_find_32_checkpoint.c ** Message: 23:20:37.986: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_cdna2genome_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_cdna2genome_32_find_32_path_32_continuation.c ** Message: 23:27:14.030: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_cdna2genome_32_find_32_score.o] ** Message: 23:27:14.030: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_cdna2genome_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_cdna2genome_32_find_32_score.o ** Message: 23:27:14.056: Adding function [optimal_58_cdna2genome_32_find_32_score] ** Message: 23:27:14.056: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_cdna2genome_32_find_32_path.o] ** Message: 23:27:14.056: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_cdna2genome_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_cdna2genome_32_find_32_path.o ** Message: 23:27:14.082: Adding function [optimal_58_cdna2genome_32_find_32_path] ** Message: 23:27:14.082: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_cdna2genome_32_find_32_region.o] ** Message: 23:27:14.082: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_cdna2genome_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_cdna2genome_32_find_32_region.o ** Message: 23:27:14.105: Adding function [optimal_58_cdna2genome_32_find_32_region] ** Message: 23:27:14.105: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_cdna2genome_32_find_32_checkpoint.o] ** Message: 23:27:14.105: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_cdna2genome_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_cdna2genome_32_find_32_checkpoint.o ** Message: 23:27:14.129: Adding function [optimal_58_cdna2genome_32_find_32_checkpoint] ** Message: 23:27:14.129: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_cdna2genome_32_find_32_path_32_continuation.o] ** Message: 23:27:14.130: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_cdna2genome_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_cdna2genome_32_find_32_path_32_continuation.o ** Message: 23:27:14.155: Adding function [optimal_58_cdna2genome_32_find_32_path_32_continuation] ** Message: 23:27:14.157: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.c ** Message: 23:27:17.151: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.c ** Message: 23:27:21.291: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o] ** Message: 23:27:21.291: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o ** Message: 23:27:21.318: Adding function [Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary] ** Message: 23:27:21.318: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o] ** Message: 23:27:21.318: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o ** Message: 23:27:21.344: Adding function [Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary] ** Message: 23:27:21.344: Compiling with: [cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -o c4_model_lookup.o -c c4_model_lookup.c] ** Message: 23:27:21.974: Adding: [c4_model_lookup.o] ** Message: 23:27:21.975: Adding object file [c4_model_lookup.o] to archive ar -Sq c4_model_archive.a c4_model_lookup.o ** Message: 23:27:22.001: Indexing archive [c4_model_archive.a] ranlib c4_model_archive.a ** Message: 23:27:22.068: Done ** Message: 23:27:22.068: Finished building bootstrapping components cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/hub -I../../src/general -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I. -DUSE_COMPILED_MODELS -c ../../src/c4/viterbi.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/hub -I../../src/general -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I. -DUSE_COMPILED_MODELS -c ../../src/sdp/scheduler.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o exonerate exonerate.o viterbi.o scheduler.o c4_model_archive.a ../../src/comparison/wordhood.o ../../src/comparison/hspset.o ../../src/comparison/seeder.o ../../src/comparison/comparison.o ../../src/database/fastapipe.o ../../src/database/fastadb.o ../../src/struct/dejavu.o ../../src/struct/fsm.o ../../src/struct/vfsm.o ../../src/struct/sparsecache.o ../../src/hub/gam.o ../../src/hub/bsam.o ../../src/hub/analysis.o ../../src/general/compoundfile.o ../../src/general/threadref.o ../../src/c4/c4.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/opair.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/layout.o ../../src/c4/region.o ../../src/c4/subopt.o ../../src/bsdp/bsdp.o ../../src/bsdp/sar.o ../../src/bsdp/heuristic.o ../../src/bsdp/hpair.o ../../src/sdp/boundary.o ../../src/sdp/sdp.o ../../src/sdp/lookahead.o ../../src/sdp/straceback.o ../../src/struct/matrix.o ../../src/struct/slist.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/translate.o ../../src/sequence/splice.o ../../src/model/affine.o ../../src/model/est2genome.o ../../src/model/ner.o ../../src/model/protein2dna.o ../../src/model/protein2genome.o ../../src/model/coding2coding.o ../../src/model/coding2genome.o ../../src/model/cdna2genome.o ../../src/model/genome2genome.o ../../src/model/ungapped.o ../../src/model/intron.o ../../src/model/frameshift.o ../../src/model/phase.o ../../src/model/modeltype.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/socket.o ../../src/general/jobqueue.o ../../src/comparison/match.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/hub -I../../src/general -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c ipcress.c ipcress.c: In function 'Ipcress_prepare_PCR': ipcress.c:264:9: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] g_strup(primer_a); ^~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:79, from ipcress.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here gchar* g_strup (gchar *string); ^~~~~~~ ipcress.c:265:9: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] g_strup(primer_b); ^~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:79, from ipcress.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here gchar* g_strup (gchar *string); ^~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o ipcress ipcress.o ../../src/comparison/pcr.o ../../src/comparison/wordhood.o ../../src/database/fastadb.o ../../src/sequence/alphabet.o ../../src/sequence/sequence.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/struct/fsm.o ../../src/struct/slist.o ../../src/struct/matrix.o ../../src/struct/recyclebin.o ../../src/struct/sparsecache.o ../../src/general/lineparse.o ../../src/general/argument.o ../../src/general/compoundfile.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/hub -I../../src/general -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c exonerate-server.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o exonerate-server exonerate-server.o ../../src/general/socket.o ../../src/general/argument.o ../../src/comparison/hspset.o ../../src/comparison/match.o ../../src/comparison/wordhood.o ../../src/database/dataset.o ../../src/database/index.o ../../src/database/fastadb.o ../../src/struct/bitarray.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/struct/splaytree.o ../../src/struct/noitree.o ../../src/struct/vfsm.o ../../src/struct/pqueue.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/translate.o ../../src/sequence/splice.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl Making all in util cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastaclean.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastaclean fastaclean.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastaclip.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastaclip fastaclip.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastachecksum.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastachecksum fastachecksum.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastacomposition.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastacomposition fastacomposition.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastadiff.c fastadiff.c: In function 'fasta_diff': fastadiff.c:70:13: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] comp = g_strcasecmp; ^~~~ In file included from /usr/local/include/glib-2.0/glib.h:79, from ../../src/general/argument.h:26, from fastadiff.c:19: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastadiff fastadiff.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastaexplode.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastaexplode fastaexplode.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastafetch.c fastafetch.c: In function 'get_query_list': fastafetch.c:121:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(query, "stdin")){ ^~ In file included from /usr/local/include/glib-2.0/glib.h:79, from ../../src/general/argument.h:26, from fastafetch.c:21: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastafetch fastafetch.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastahardmask.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastahardmask fastahardmask.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastaindex.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastaindex fastaindex.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastalength.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastalength fastalength.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastanrdb.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastanrdb fastanrdb.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastaoverlap.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastaoverlap fastaoverlap.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastareformat.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastareformat fastareformat.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastaremove.c fastaremove.c: In function 'Argument_main': fastaremove.c:73:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(remove_path, "stdin")){ ^~ In file included from /usr/local/include/glib-2.0/glib.h:79, from ../../src/general/argument.h:26, from fastaremove.c:19: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastaremove fastaremove.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastarevcomp.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastarevcomp fastarevcomp.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastasoftmask.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastasoftmask fastasoftmask.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastasort.c fastasort.c: In function 'SortKey_Mask_create': fastasort.c:130:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(sort_key, "id")) ^~ In file included from /usr/local/include/glib-2.0/glib.h:79, from ../../src/general/argument.h:26, from fastasort.c:20: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ fastasort.c:132:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] else if(!g_strcasecmp(sort_key, "len")) ^~~~ In file included from /usr/local/include/glib-2.0/glib.h:79, from ../../src/general/argument.h:26, from fastasort.c:20: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ fastasort.c:134:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] else if(!g_strcasecmp(sort_key, "seq")) ^~~~ In file included from /usr/local/include/glib-2.0/glib.h:79, from ../../src/general/argument.h:26, from fastasort.c:20: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastasort fastasort.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastasplit.c fastasplit.c: In function 'Argument_main': fastasplit.c:92:13: warning: 'g_basename' is deprecated: Use 'g_path_get_basename' instead [-Wdeprecated-declarations] output_dir, G_DIR_SEPARATOR, g_basename(query_path)); ^~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:48, from ../../src/general/argument.h:26, from fastasplit.c:20: /usr/local/include/glib-2.0/glib/gfileutils.h:163:14: note: declared here const gchar *g_basename (const gchar *file_name); ^~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastasplit fastasplit.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastasubseq.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastasubseq fastasubseq.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastatranslate.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastatranslate fastatranslate.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastavalidcds.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastavalidcds fastavalidcds.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fasta2esd.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fasta2esd fasta2esd.o ../../src/database/dataset.o ../../src/struct/bitarray.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastaannotatecdna.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastaannotatecdna fastaannotatecdna.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c esd2esi.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o esd2esi esd2esi.o ../../src/database/dataset.o ../../src/database/index.o ../../src/general/threadref.o ../../src/struct/bitarray.o ../../src/struct/vfsm.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/struct/noitree.o ../../src/struct/splaytree.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/comparison/wordhood.o ../../src/comparison/hspset.o ../../src/comparison/match.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl Making all in test Making all in data Making all in cdna Making all in protein Making all in exonerate Making all in ipcress Making all in util SUCCEEDED 00:29:31 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for exonerate-2.4.0 ===> Generating temporary packing list Making install in doc Making install in man Making install in man1 /usr/bin/make install-man1 /bin/sh ../../../mkinstalldirs /construction/biology/exonerate/stage/usr/local/man/man1 install -m 0644 ./exonerate.1 /construction/biology/exonerate/stage/usr/local/man/man1/exonerate.1 install -m 0644 ./ipcress.1 /construction/biology/exonerate/stage/usr/local/man/man1/ipcress.1 install -m 0644 ./exonerate-server.1 /construction/biology/exonerate/stage/usr/local/man/man1/exonerate-server.1 install -m 0644 ./fastautils.1 /construction/biology/exonerate/stage/usr/local/man/man1/fastautils.1 Making install in src Making install in struct Making install in general Making install in sequence Making install in comparison Making install in database Making install in c4 Making install in bsdp Making install in sdp Making install in model Making install in hub Making install in program /bin/sh ../../mkinstalldirs /construction/biology/exonerate/stage/usr/local/bin install -s -m 555 exonerate /construction/biology/exonerate/stage/usr/local/bin/exonerate install -s -m 555 ipcress /construction/biology/exonerate/stage/usr/local/bin/ipcress install -s -m 555 exonerate-server /construction/biology/exonerate/stage/usr/local/bin/exonerate-server Making install in util /bin/sh ../../mkinstalldirs /construction/biology/exonerate/stage/usr/local/bin install -s -m 555 fastaclean /construction/biology/exonerate/stage/usr/local/bin/fastaclean install -s -m 555 fastaclip /construction/biology/exonerate/stage/usr/local/bin/fastaclip install -s -m 555 fastachecksum /construction/biology/exonerate/stage/usr/local/bin/fastachecksum install -s -m 555 fastacomposition /construction/biology/exonerate/stage/usr/local/bin/fastacomposition install -s -m 555 fastadiff /construction/biology/exonerate/stage/usr/local/bin/fastadiff install -s -m 555 fastaexplode /construction/biology/exonerate/stage/usr/local/bin/fastaexplode install -s -m 555 fastafetch /construction/biology/exonerate/stage/usr/local/bin/fastafetch install -s -m 555 fastahardmask /construction/biology/exonerate/stage/usr/local/bin/fastahardmask install -s -m 555 fastaindex /construction/biology/exonerate/stage/usr/local/bin/fastaindex install -s -m 555 fastalength /construction/biology/exonerate/stage/usr/local/bin/fastalength install -s -m 555 fastanrdb /construction/biology/exonerate/stage/usr/local/bin/fastanrdb install -s -m 555 fastaoverlap /construction/biology/exonerate/stage/usr/local/bin/fastaoverlap install -s -m 555 fastareformat /construction/biology/exonerate/stage/usr/local/bin/fastareformat install -s -m 555 fastaremove /construction/biology/exonerate/stage/usr/local/bin/fastaremove install -s -m 555 fastarevcomp /construction/biology/exonerate/stage/usr/local/bin/fastarevcomp install -s -m 555 fastasoftmask /construction/biology/exonerate/stage/usr/local/bin/fastasoftmask install -s -m 555 fastasort /construction/biology/exonerate/stage/usr/local/bin/fastasort install -s -m 555 fastasplit /construction/biology/exonerate/stage/usr/local/bin/fastasplit install -s -m 555 fastasubseq /construction/biology/exonerate/stage/usr/local/bin/fastasubseq install -s -m 555 fastatranslate /construction/biology/exonerate/stage/usr/local/bin/fastatranslate install -s -m 555 fastavalidcds /construction/biology/exonerate/stage/usr/local/bin/fastavalidcds install -s -m 555 fasta2esd /construction/biology/exonerate/stage/usr/local/bin/fasta2esd install -s -m 555 fastaannotatecdna /construction/biology/exonerate/stage/usr/local/bin/fastaannotatecdna install -s -m 555 esd2esi /construction/biology/exonerate/stage/usr/local/bin/esd2esi Making install in test Making install in data Making install in cdna Making install in protein Making install in exonerate Making install in ipcress Making install in util ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:04 ------------------------------------------------------------------------------- -- Phase: check-plist ------------------------------------------------------------------------------- ====> Checking for pkg-plist issues (check-plist) ===> Parsing plist ===> Checking for items in STAGEDIR missing from pkg-plist ===> Checking for items in pkg-plist which are not in STAGEDIR ===> No pkg-plist issues found (check-plist) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for exonerate-2.4.0 file sizes/checksums [31]: 0% file sizes/checksums [31]: 100% packing files [31]: 0% packing files [31]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:17 TOTAL TIME 00:30:17