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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 Making all in doc make[1]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/doc' Making all in man make[2]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/doc/man' Making all in man1 make[3]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/doc/man/man1' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/doc/man/man1' make[3]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/doc/man' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/doc/man' make[2]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/doc/man' make[2]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/doc' make[2]: Nothing to be done for 'all-am'. make[2]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/doc' make[1]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/doc' Making all in src make[1]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src' Making all in struct make[2]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct' gcc -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="\"llu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fsm.test.c gcc -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="\"llu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fsm.c gcc -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="\"llu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c recyclebin.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fsm.test fsm.test.o fsm.o recyclebin.o -lglib-2.0 gcc -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="\"llu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c matrix.test.c gcc -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="\"llu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c matrix.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o matrix.test matrix.test.o matrix.o -lglib-2.0 gcc -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="\"llu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c pqueue.test.c gcc -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="\"llu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c pqueue.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o pqueue.test pqueue.test.o pqueue.o recyclebin.o -lglib-2.0 gcc -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="\"llu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c slist.test.c gcc -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="\"llu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c slist.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o slist.test slist.test.o slist.o recyclebin.o -lglib-2.0 gcc -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="\"llu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c rangetree.test.c gcc -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="\"llu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/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] 151 | g_tree_traverse(rt->recent_data, RangeTree_insert_recent_collect, | ^~~~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:92, from rangetree.h:23, from rangetree.c:18: /usr/include/glib-2.0/glib/gtree.h:146:10: note: declared here 146 | void g_tree_traverse (GTree *tree, | ^~~~~~~~~~~~~~~ gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o rangetree.test rangetree.test.o rangetree.o recyclebin.o -lglib-2.0 gcc -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="\"llu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c vfsm.test.c gcc -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="\"llu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c vfsm.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o vfsm.test vfsm.test.o vfsm.o -lm -lglib-2.0 gcc -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="\"llu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c recyclebin.test.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o recyclebin.test recyclebin.test.o recyclebin.o -lglib-2.0 gcc -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="\"llu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c sparsecache.test.c gcc -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="\"llu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c sparsecache.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o sparsecache.test sparsecache.test.o sparsecache.o -lglib-2.0 gcc -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="\"llu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c dejavu.test.c gcc -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="\"llu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c dejavu.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o dejavu.test dejavu.test.o dejavu.o -lglib-2.0 gcc -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="\"llu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c bitarray.test.c gcc -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="\"llu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c bitarray.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o bitarray.test bitarray.test.o bitarray.o -lglib-2.0 gcc -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="\"llu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c splaytree.test.c gcc -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="\"llu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c splaytree.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o splaytree.test splaytree.test.o splaytree.o recyclebin.o -lglib-2.0 gcc -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="\"llu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c noitree.test.c gcc -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="\"llu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c noitree.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o noitree.test noitree.test.o noitree.o recyclebin.o splaytree.o -lglib-2.0 make[2]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct' Making all in general make[2]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general' gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c argument.test.c gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/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] 138 | if(!g_strcasecmp(arg_string, true_string[i])) | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from argument.h:26, from argument.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ argument.c:140:9: warning: ‘g_strcasecmp’ is deprecated [-Wdeprecated-declarations] 140 | if(!g_strcasecmp(arg_string, false_string[i])) | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from argument.h:26, from argument.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ argument.c: In function ‘main’: argument.c:306:13: warning: Deprecated pre-processor symbol 306 | if(!g_thread_supported()) | ^~~~~~~~~~~~~~~~~ argument.c:307:9: warning: ‘g_thread_init’ is deprecated [-Wdeprecated-declarations] 307 | g_thread_init(NULL); | ^~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:112, from argument.h:26, from argument.c:16: /usr/include/glib-2.0/glib/deprecated/gthread.h:265:10: note: declared here 265 | void g_thread_init (gpointer vtable); | ^~~~~~~~~~~~~ argument.c: In function ‘Argument_process’: argument.c:502:5: warning: ‘g_tree_traverse’ is deprecated [-Wdeprecated-declarations] 502 | g_tree_traverse(arg->option_registry, Argument_set_env_var_func, | ^~~~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:92, from argument.h:26, from argument.c:16: /usr/include/glib-2.0/glib/gtree.h:146:10: note: declared here 146 | void g_tree_traverse (GTree *tree, | ^~~~~~~~~~~~~~~ argument.c:559:5: warning: ‘g_tree_traverse’ is deprecated [-Wdeprecated-declarations] 559 | g_tree_traverse(arg->option_registry, | ^~~~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:92, from argument.h:26, from argument.c:16: /usr/include/glib-2.0/glib/gtree.h:146:10: note: declared here 146 | void g_tree_traverse (GTree *tree, | ^~~~~~~~~~~~~~~ gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o argument.test argument.test.o argument.o -lglib-2.0 gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c lineparse.test.c gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c lineparse.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o lineparse.test lineparse.test.o lineparse.o -lglib-2.0 gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c compoundfile.test.c gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c compoundfile.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o compoundfile.test compoundfile.test.o compoundfile.o -lglib-2.0 gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c socket.test.c gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c socket.c socket.c: In function ‘Socket_send’: socket.c:168:13: warning: Deprecated pre-processor symbol: replace with "g_string_append_printf" 168 | g_string_sprintfa(full_msg, "linecount: %d\n", line_count+1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ socket.c:169:13: warning: Deprecated pre-processor symbol: replace with "g_string_append_printf" 169 | g_string_sprintfa(full_msg, "%s", msg); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o socket.test socket.test.o socket.o -lglib-2.0 gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/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:34:13: warning: Deprecated pre-processor symbol 34 | if(!g_thread_supported()) | ^~~~~~~~~~~~~~~~~ jobqueue.test.c:35:9: warning: ‘g_thread_init’ is deprecated [-Wdeprecated-declarations] 35 | g_thread_init(NULL); | ^~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:112, from jobqueue.h:23, from jobqueue.test.c:17: /usr/include/glib-2.0/glib/deprecated/gthread.h:265:10: note: declared here 265 | void g_thread_init (gpointer vtable); | ^~~~~~~~~~~~~ gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c jobqueue.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o jobqueue.test jobqueue.test.o jobqueue.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o -lglib-2.0 gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c threadref.test.c gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c threadref.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o threadref.test threadref.test.o threadref.o -lpthread -lglib-2.0 make[2]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general' Making all in sequence make[2]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence' gcc -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 -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c sequence.test.c gcc -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 -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/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] 97 | g_tree_traverse(tree, Sequence_destroy_annotation_data, | ^~~~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:92, from sequence.h:24, from sequence.c:21: /usr/include/glib-2.0/glib/gtree.h:146:10: note: declared here 146 | void g_tree_traverse (GTree *tree, | ^~~~~~~~~~~~~~~ gcc -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 -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/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] 317 | if(!g_strcasecmp(name, dna_string[i])) | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from alphabet.h:24, from alphabet.c:19: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ alphabet.c:320:9: warning: ‘g_strcasecmp’ is deprecated [-Wdeprecated-declarations] 320 | if(!g_strcasecmp(name, protein_string[i])) | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from alphabet.h:24, from alphabet.c:19: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ alphabet.c:323:9: warning: ‘g_strcasecmp’ is deprecated [-Wdeprecated-declarations] 323 | if(!g_strcasecmp(name, unknown_string[i])) | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from alphabet.h:24, from alphabet.c:19: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ gcc -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 -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c translate.c gcc -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 -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/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] 146 | if(!g_strcasecmp(word, "splice")) | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from splice.h:23, from splice.c:22: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | 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] 195 | if((!path) || (!strlen(path)) || (!g_strcasecmp(path, "primate"))) | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from splice.h:23, from splice.c:22: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | 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] 203 | if((!path) || (!strlen(path)) || (!g_strcasecmp(path, "primate"))) | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from splice.h:23, from splice.c:22: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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 -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c submat.test.c gcc -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 -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c submat.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o submat.test submat.test.o submat.o -lglib-2.0 gcc -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 -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c translate.test.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o translate.test translate.test.o translate.o ../../src/general/argument.o -lglib-2.0 gcc -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 -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c splice.test.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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 -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c alphabet.test.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o alphabet.test alphabet.test.o alphabet.o ../../src/general/argument.o -lglib-2.0 gcc -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 -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c codonsubmat.test.c gcc -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 -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c codonsubmat.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o codonsubmat.test codonsubmat.test.o codonsubmat.o ../../src/general/argument.o -lm -lglib-2.0 make[2]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence' Making all in comparison make[2]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison' gcc -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 -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c wordhood.test.c gcc -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 -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c wordhood.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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 -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c hspset.test.c gcc -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 -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/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] 637 | g_strdown(query_str); | ^~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:82, from hspset.h:26, from hspset.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:208:23: note: declared here 208 | gchar* g_strdown (gchar *string); | ^~~~~~~~~ hspset.c:638:9: warning: ‘g_strdown’ is deprecated [-Wdeprecated-declarations] 638 | g_strdown(target_str); | ^~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:82, from hspset.h:26, from hspset.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:208:23: note: declared here 208 | gchar* g_strdown (gchar *string); | ^~~~~~~~~ hspset.c:640:9: warning: ‘g_strup’ is deprecated [-Wdeprecated-declarations] 640 | g_strup(query_str); | ^~~~~~~ In file included from /usr/include/glib-2.0/glib.h:82, from hspset.h:26, from hspset.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here 210 | gchar* g_strup (gchar *string); | ^~~~~~~ hspset.c:641:9: warning: ‘g_strup’ is deprecated [-Wdeprecated-declarations] 641 | g_strup(target_str); | ^~~~~~~ In file included from /usr/include/glib-2.0/glib.h:82, from hspset.h:26, from hspset.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here 210 | gchar* g_strup (gchar *string); | ^~~~~~~ gcc -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 -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c match.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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 -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c pcr.test.c gcc -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 -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/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] 31 | pcr_match = g_chunk_new(PCR_Match, pcr->match_mem_chunk); | ^~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:107, from pcr.h:23, from pcr.c:16: /usr/include/glib-2.0/glib/deprecated/gallocator.h:50:17: note: declared here 50 | 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] 59 | register PCR_Probe *pcr_probe = g_chunk_new(PCR_Probe, | ^~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:107, from pcr.h:23, from pcr.c:16: /usr/include/glib-2.0/glib/deprecated/gallocator.h:50:17: note: declared here 50 | 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] 69 | g_mem_chunk_free(pcr->probe_mem_chunk, pcr_probe); | ^~~~~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:107, from pcr.h:23, from pcr.c:16: /usr/include/glib-2.0/glib/deprecated/gallocator.h:54:17: note: declared here 54 | 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] 155 | register PCR_Sensor *pcr_sensor = g_chunk_new(PCR_Sensor, | ^~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:107, from pcr.h:23, from pcr.c:16: /usr/include/glib-2.0/glib/deprecated/gallocator.h:50:17: note: declared here 50 | 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] 174 | g_mem_chunk_free(pcr->sensor_mem_chunk, pcr_sensor); | ^~~~~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:107, from pcr.h:23, from pcr.c:16: /usr/include/glib-2.0/glib/deprecated/gallocator.h:54:17: note: declared here 54 | 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] 252 | g_strup(pcr_primer->forward); | ^~~~~~~ In file included from /usr/include/glib-2.0/glib.h:82, from pcr.h:23, from pcr.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here 210 | gchar* g_strup (gchar *string); | ^~~~~~~ pcr.c:253:5: warning: ‘g_strup’ is deprecated [-Wdeprecated-declarations] 253 | g_strup(pcr_primer->revcomp); | ^~~~~~~ In file included from /usr/include/glib-2.0/glib.h:82, from pcr.h:23, from pcr.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here 210 | gchar* g_strup (gchar *string); | ^~~~~~~ pcr.c: In function ‘PCR_create’: pcr.c:357:5: warning: ‘g_mem_chunk_new’ is deprecated [-Wdeprecated-declarations] 357 | pcr->sensor_mem_chunk = g_mem_chunk_new("PCR_Sensor", | ^~~ In file included from /usr/include/glib-2.0/glib.h:107, from pcr.h:23, from pcr.c:16: /usr/include/glib-2.0/glib/deprecated/gallocator.h:43:17: note: declared here 43 | GMemChunk * g_mem_chunk_new (const gchar *name, | ^~~~~~~~~~~~~~~ pcr.c:363:5: warning: ‘g_mem_chunk_new’ is deprecated [-Wdeprecated-declarations] 363 | pcr->probe_mem_chunk = g_mem_chunk_new("PCR_Probe", | ^~~ In file included from /usr/include/glib-2.0/glib.h:107, from pcr.h:23, from pcr.c:16: /usr/include/glib-2.0/glib/deprecated/gallocator.h:43:17: note: declared here 43 | GMemChunk * g_mem_chunk_new (const gchar *name, | ^~~~~~~~~~~~~~~ pcr.c:366:5: warning: ‘g_mem_chunk_new’ is deprecated [-Wdeprecated-declarations] 366 | pcr->match_mem_chunk = g_mem_chunk_new("PCR_Match", | ^~~ In file included from /usr/include/glib-2.0/glib.h:107, from pcr.h:23, from pcr.c:16: /usr/include/glib-2.0/glib/deprecated/gallocator.h:43:17: note: declared here 43 | 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] 381 | g_mem_chunk_destroy(pcr->sensor_mem_chunk); | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:107, from pcr.h:23, from pcr.c:16: /usr/include/glib-2.0/glib/deprecated/gallocator.h:48:17: note: declared here 48 | void g_mem_chunk_destroy (GMemChunk *mem_chunk); | ^~~~~~~~~~~~~~~~~~~ pcr.c:383:5: warning: ‘g_mem_chunk_destroy’ is deprecated [-Wdeprecated-declarations] 383 | g_mem_chunk_destroy(pcr->probe_mem_chunk); | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:107, from pcr.h:23, from pcr.c:16: /usr/include/glib-2.0/glib/deprecated/gallocator.h:48:17: note: declared here 48 | void g_mem_chunk_destroy (GMemChunk *mem_chunk); | ^~~~~~~~~~~~~~~~~~~ pcr.c:384:5: warning: ‘g_mem_chunk_destroy’ is deprecated [-Wdeprecated-declarations] 384 | g_mem_chunk_destroy(pcr->match_mem_chunk); | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:107, from pcr.h:23, from pcr.c:16: /usr/include/glib-2.0/glib/deprecated/gallocator.h:48:17: note: declared here 48 | void g_mem_chunk_destroy (GMemChunk *mem_chunk); | ^~~~~~~~~~~~~~~~~~~ gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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 -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c comparison.test.c gcc -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 -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c comparison.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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 -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c match.test.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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 -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c seeder.test.c gcc -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 -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/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] 268 | if(!g_strcasecmp(force_fsm, "none")) | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from seeder.h:23, from seeder.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ seeder.c:273:5: warning: ‘g_strcasecmp’ is deprecated [-Wdeprecated-declarations] 273 | if(!g_strcasecmp(force_fsm, "normal")) | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from seeder.h:23, from seeder.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ seeder.c:275:5: warning: ‘g_strcasecmp’ is deprecated [-Wdeprecated-declarations] 275 | if(!g_strcasecmp(force_fsm, "compact")) | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from seeder.h:23, from seeder.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 make[2]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison' Making all in database make[2]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/database' gcc -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="\"llu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastadb.test.c gcc -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="\"llu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastadb.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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="\"llu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastapipe.test.c gcc -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="\"llu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastapipe.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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="\"llu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c dataset.test.c gcc -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="\"llu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c dataset.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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="\"llu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c index.test.c gcc -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="\"llu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c index.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 make[2]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/database' Making all in c4 make[2]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4' gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -DHOSTTYPE="\"i586-slackware-linux-gnu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c region.test.c gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -DHOSTTYPE="\"i586-slackware-linux-gnu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c region.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o region.test region.test.o region.o -lglib-2.0 gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -DHOSTTYPE="\"i586-slackware-linux-gnu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c c4.test.c gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -DHOSTTYPE="\"i586-slackware-linux-gnu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c c4.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o c4.test c4.test.o c4.o region.o ../../src/struct/matrix.o ../../src/general/threadref.o -lglib-2.0 gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -DHOSTTYPE="\"i586-slackware-linux-gnu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c alignment.test.c gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -DHOSTTYPE="\"i586-slackware-linux-gnu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/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] 660 | g_strdown(qy_seq_string); | ^~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:82, from ../../src/comparison/match.h:23, from alignment.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:208:23: note: declared here 208 | gchar* g_strdown (gchar *string); | ^~~~~~~~~ alignment.c:667:9: warning: ‘g_strdown’ is deprecated [-Wdeprecated-declarations] 667 | g_strdown(tg_seq_string); | ^~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:82, from ../../src/comparison/match.h:23, from alignment.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:208:23: note: declared here 208 | gchar* g_strdown (gchar *string); | ^~~~~~~~~ alignment.c:677:13: warning: ‘g_strdown’ is deprecated [-Wdeprecated-declarations] 677 | g_strdown(qy_seq_string); | ^~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:82, from ../../src/comparison/match.h:23, from alignment.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:208:23: note: declared here 208 | gchar* g_strdown (gchar *string); | ^~~~~~~~~ alignment.c:690:9: warning: ‘g_strdown’ is deprecated [-Wdeprecated-declarations] 690 | g_strdown(tg_seq_string); | ^~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:82, from ../../src/comparison/match.h:23, from alignment.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:208:23: note: declared here 208 | gchar* g_strdown (gchar *string); | ^~~~~~~~~ alignment.c: In function ‘AlignmentView_add_SPLIT_CODON’: alignment.c:987:5: warning: ‘g_strup’ is deprecated [-Wdeprecated-declarations] 987 | g_strup(qy_codon); | ^~~~~~~ In file included from /usr/include/glib-2.0/glib.h:82, from ../../src/comparison/match.h:23, from alignment.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here 210 | gchar* g_strup (gchar *string); | ^~~~~~~ alignment.c:988:5: warning: ‘g_strup’ is deprecated [-Wdeprecated-declarations] 988 | g_strup(tg_codon); | ^~~~~~~ In file included from /usr/include/glib-2.0/glib.h:82, from ../../src/comparison/match.h:23, from alignment.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here 210 | gchar* g_strup (gchar *string); | ^~~~~~~ gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -DHOSTTYPE="\"i586-slackware-linux-gnu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c codegen.test.c gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -DHOSTTYPE="\"i586-slackware-linux-gnu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c codegen.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o codegen.test codegen.test.o codegen.o ../../src/general/argument.o -lglib-2.0 gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -DHOSTTYPE="\"i586-slackware-linux-gnu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c optimal.test.c gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -DHOSTTYPE="\"i586-slackware-linux-gnu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c optimal.c gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -DHOSTTYPE="\"i586-slackware-linux-gnu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c layout.c gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -DHOSTTYPE="\"i586-slackware-linux-gnu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c viterbi.c gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -DHOSTTYPE="\"i586-slackware-linux-gnu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c subopt.c gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -DHOSTTYPE="\"i586-slackware-linux-gnu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c cgutil.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -DHOSTTYPE="\"i586-slackware-linux-gnu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c layout.test.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o layout.test layout.test.o layout.o ../../src/struct/matrix.o -lglib-2.0 gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -DHOSTTYPE="\"i586-slackware-linux-gnu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c viterbi.test.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -DHOSTTYPE="\"i586-slackware-linux-gnu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c opair.test.c gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -DHOSTTYPE="\"i586-slackware-linux-gnu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c opair.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -DHOSTTYPE="\"i586-slackware-linux-gnu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c subopt.test.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o subopt.test subopt.test.o subopt.o region.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o -lglib-2.0 gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -DHOSTTYPE="\"i586-slackware-linux-gnu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c cgutil.test.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 make[2]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4' Making all in bsdp make[2]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp' gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -DHOSTTYPE="\"i586-slackware-linux-gnu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c heuristic.test.c gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -DHOSTTYPE="\"i586-slackware-linux-gnu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c heuristic.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -DHOSTTYPE="\"i586-slackware-linux-gnu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c bsdp.test.c gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -DHOSTTYPE="\"i586-slackware-linux-gnu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c bsdp.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o bsdp.test bsdp.test.o bsdp.o ../../src/general/argument.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o -lglib-2.0 gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -DHOSTTYPE="\"i586-slackware-linux-gnu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c hpair.test.c gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -DHOSTTYPE="\"i586-slackware-linux-gnu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c hpair.c gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -DHOSTTYPE="\"i586-slackware-linux-gnu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c sar.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -DHOSTTYPE="\"i586-slackware-linux-gnu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c sar.test.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 make[2]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp' Making all in sdp make[2]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp' gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -DHOSTTYPE="\"i586-slackware-linux-gnu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c sdp.test.c gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -DHOSTTYPE="\"i586-slackware-linux-gnu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c sdp.c gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -DHOSTTYPE="\"i586-slackware-linux-gnu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c boundary.c gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -DHOSTTYPE="\"i586-slackware-linux-gnu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c scheduler.c gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -DHOSTTYPE="\"i586-slackware-linux-gnu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c lookahead.c gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -DHOSTTYPE="\"i586-slackware-linux-gnu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c straceback.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -DHOSTTYPE="\"i586-slackware-linux-gnu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c lookahead.test.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o lookahead.test lookahead.test.o lookahead.o -lglib-2.0 gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -DHOSTTYPE="\"i586-slackware-linux-gnu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c boundary.test.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o boundary.test boundary.test.o boundary.o ../../src/general/argument.o ../../src/c4/region.o -lglib-2.0 gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -DHOSTTYPE="\"i586-slackware-linux-gnu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c scheduler.test.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -DHOSTTYPE="\"i586-slackware-linux-gnu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c straceback.test.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 make[2]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp' Making all in model make[2]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model' gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c edit_distance.test.c gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c edit_distance.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c affine.test.c gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c affine.c gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c ungapped.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c protein2dna.test.c gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c protein2dna.c gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c frameshift.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c ner.test.c gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c ner.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c est2genome.test.c gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c est2genome.c gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c intron.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c ungapped.test.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c intron.test.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c protein2genome.test.c gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c protein2genome.c gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c phase.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c coding2coding.test.c gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c coding2coding.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c frameshift.test.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c coding2genome.test.c gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c coding2genome.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c cdna2genome.test.c gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c cdna2genome.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c genome2genome.test.c gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c genome2genome.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c phase.test.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c modeltype.test.c gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/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] 121 | if(!g_strcasecmp(name[i], str)) | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from ../../src/c4/c4.h:23, from modeltype.h:23, from modeltype.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ modeltype.c:124:9: warning: ‘g_strcasecmp’ is deprecated [-Wdeprecated-declarations] 124 | if(!g_strcasecmp(short_name[i], str)) | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from ../../src/c4/c4.h:23, from modeltype.h:23, from modeltype.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/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] 421 | if((!models) || (!g_strcasecmp(models, "all"))) | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from ../../src/c4/c4.h:23, from ungapped.h:23, from bootstrapper.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 make[2]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model' Making all in hub make[2]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/hub' gcc -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="\"i586-slackware-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c gam.test.c gcc -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="\"i586-slackware-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/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] 68 | if(!g_strcasecmp(name[i], str)) | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from gam.h:23, from gam.c:21: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | 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] 526 | g_tree_traverse(bestn_tree, GAM_tree_collect_values, | ^~~~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:92, from gam.h:23, from gam.c:21: /usr/include/glib-2.0/glib/gtree.h:146:10: note: declared here 146 | 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] 539 | g_tree_traverse(percent_threshold_tree, GAM_tree_collect_values, | ^~~~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:92, from gam.h:23, from gam.c:21: /usr/include/glib-2.0/glib/gtree.h:146:10: note: declared here 146 | void g_tree_traverse (GTree *tree, | ^~~~~~~~~~~~~~~ gam.c: In function ‘GAM_report’: gam.c:589:9: warning: ‘g_tree_traverse’ is deprecated [-Wdeprecated-declarations] 589 | g_tree_traverse(gam->bestn_tree, GAM_bestn_tree_report_traverse, | ^~~~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:92, from gam.h:23, from gam.c:21: /usr/include/glib-2.0/glib/gtree.h:146:10: note: declared here 146 | void g_tree_traverse (GTree *tree, | ^~~~~~~~~~~~~~~ gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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="\"i586-slackware-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c analysis.test.c gcc -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="\"i586-slackware-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/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] 329 | if(!g_strcasecmp(force_scan, "none")){ | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from analysis.h:23, from analysis.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ analysis.c:336:5: warning: ‘g_strcasecmp’ is deprecated [-Wdeprecated-declarations] 336 | } else if((!g_strcasecmp(force_scan, "query")) | ^ In file included from /usr/include/glib-2.0/glib.h:82, from analysis.h:23, from analysis.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ analysis.c:337:12: warning: ‘g_strcasecmp’ is deprecated [-Wdeprecated-declarations] 337 | || (!g_strcasecmp(force_scan, "q"))){ | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from analysis.h:23, from analysis.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ analysis.c:339:5: warning: ‘g_strcasecmp’ is deprecated [-Wdeprecated-declarations] 339 | } else if((!g_strcasecmp(force_scan, "target")) | ^ In file included from /usr/include/glib-2.0/glib.h:82, from analysis.h:23, from analysis.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ analysis.c:340:12: warning: ‘g_strcasecmp’ is deprecated [-Wdeprecated-declarations] 340 | || (!g_strcasecmp(force_scan, "t"))){ | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from analysis.h:23, from analysis.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ gcc -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="\"i586-slackware-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c bsam.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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="\"i586-slackware-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c bsam.test.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 make[2]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/hub' Making all in program make[2]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/program' gcc -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="\"i586-slackware-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/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: 00:35:45.842: Starting building bootstrapping components ** Message: 00:35:45.843: Processing model [u] ** Message: 00:35:45.844: Bootstrapper processing model [ungapped:dna2dna] ** Message: 00:35:45.844: Process optimal [optimal:ungapped:dna2dna] ** (process:22106): WARNING **: 00:35:45.844: Creating codegen directory [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen] ** (process:22106): WARNING **: 00:35:45.844: Creating codegen directory [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen] ** (process:22106): WARNING **: 00:35:45.844: Creating codegen directory [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu] ** (process:22106): WARNING **: 00:35:45.844: Creating codegen directory [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu] ** Message: 00:35:45.844: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_score.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_score.c ** Message: 00:35:45.928: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path.c ** Message: 00:35:46.023: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_region.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_region.c ** Message: 00:35:46.124: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.c: In function ‘optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint’: /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.c:32:25: warning: variable ‘transition’ set but not used [-Wunused-but-set-variable] 32 | register C4_Transition *transition; | ^~~~~~~~~~ ** Message: 00:35:46.261: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 00:35:46.400: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_score.o] ** Message: 00:35:46.400: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_score.o] to archive ar -cSq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_score.o ** Message: 00:35:46.404: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_score] ** Message: 00:35:46.404: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path.o] ** Message: 00:35:46.404: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path.o ** Message: 00:35:46.408: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_path] ** Message: 00:35:46.408: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_region.o] ** Message: 00:35:46.408: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_region.o ** Message: 00:35:46.412: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_region] ** Message: 00:35:46.412: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.o] ** Message: 00:35:46.412: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.o ** Message: 00:35:46.416: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint] ** Message: 00:35:46.416: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 00:35:46.416: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 00:35:46.420: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation] ** Message: 00:35:46.420: Bootstrapper processing model [ungapped:protein2protein] ** Message: 00:35:46.420: Process optimal [optimal:ungapped:protein2protein] ** Message: 00:35:46.421: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_score.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_score.c ** Message: 00:35:46.503: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path.c ** Message: 00:35:46.595: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_region.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_region.c ** Message: 00:35:46.692: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.c: In function ‘optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint’: /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.c:32:25: warning: variable ‘transition’ set but not used [-Wunused-but-set-variable] 32 | register C4_Transition *transition; | ^~~~~~~~~~ ** Message: 00:35:46.823: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.c ** Message: 00:35:46.956: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_score.o] ** Message: 00:35:46.956: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_score.o ** Message: 00:35:46.960: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_score] ** Message: 00:35:46.960: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path.o] ** Message: 00:35:46.960: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path.o ** Message: 00:35:46.964: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_path] ** Message: 00:35:46.964: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_region.o] ** Message: 00:35:46.964: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_region.o ** Message: 00:35:46.968: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_region] ** Message: 00:35:46.968: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.o] ** Message: 00:35:46.968: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.o ** Message: 00:35:46.972: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint] ** Message: 00:35:46.972: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.o] ** Message: 00:35:46.972: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.o ** Message: 00:35:46.977: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation] ** Message: 00:35:46.977: Bootstrapper processing model [ungapped:dna2protein] ** Message: 00:35:46.977: Process optimal [optimal:ungapped:dna2protein] ** Message: 00:35:46.977: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_score.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_score.c ** Message: 00:35:47.076: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path.c ** Message: 00:35:47.196: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_region.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_region.c ** Message: 00:35:47.330: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.c: In function ‘optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint’: /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.c:32:25: warning: variable ‘transition’ set but not used [-Wunused-but-set-variable] 32 | register C4_Transition *transition; | ^~~~~~~~~~ ** Message: 00:35:47.490: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.c ** Message: 00:35:47.657: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_score.o] ** Message: 00:35:47.657: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_score.o ** Message: 00:35:47.661: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_score] ** Message: 00:35:47.661: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path.o] ** Message: 00:35:47.661: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path.o ** Message: 00:35:47.665: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_path] ** Message: 00:35:47.665: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_region.o] ** Message: 00:35:47.665: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_region.o ** Message: 00:35:47.670: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_region] ** Message: 00:35:47.670: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.o] ** Message: 00:35:47.670: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.o ** Message: 00:35:47.674: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint] ** Message: 00:35:47.674: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.o] ** Message: 00:35:47.674: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.o ** Message: 00:35:47.678: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation] ** Message: 00:35:47.678: Bootstrapper processing model [ungapped:protein2dna] ** Message: 00:35:47.678: Process optimal [optimal:ungapped:protein2dna] ** Message: 00:35:47.678: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_score.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_score.c ** Message: 00:35:47.775: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path.c ** Message: 00:35:47.885: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_region.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_region.c ** Message: 00:35:48.005: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.c: In function ‘optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint’: /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.c:34:25: warning: variable ‘transition’ set but not used [-Wunused-but-set-variable] 34 | register C4_Transition *transition; | ^~~~~~~~~~ ** Message: 00:35:48.189: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.c ** Message: 00:35:48.354: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_score.o] ** Message: 00:35:48.354: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_score.o ** Message: 00:35:48.359: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_score] ** Message: 00:35:48.359: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path.o] ** Message: 00:35:48.359: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path.o ** Message: 00:35:48.363: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_path] ** Message: 00:35:48.363: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_region.o] ** Message: 00:35:48.363: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_region.o ** Message: 00:35:48.367: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_region] ** Message: 00:35:48.367: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.o] ** Message: 00:35:48.367: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.o ** Message: 00:35:48.371: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint] ** Message: 00:35:48.371: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.o] ** Message: 00:35:48.371: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.o ** Message: 00:35:48.375: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation] ** Message: 00:35:48.375: Processing model [u:t] ** Message: 00:35:48.375: Bootstrapper processing model [ungapped:codon] ** Message: 00:35:48.375: Process optimal [optimal:ungapped:codon] ** Message: 00:35:48.376: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_score.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_score.c ** Message: 00:35:48.507: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path.c ** Message: 00:35:48.669: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_region.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_region.c ** Message: 00:35:48.859: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_checkpoint.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_checkpoint.c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_checkpoint.c: In function ‘optimal_58_ungapped_58_codon_32_find_32_checkpoint’: /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_checkpoint.c:34:25: warning: variable ‘transition’ set but not used [-Wunused-but-set-variable] 34 | register C4_Transition *transition; | ^~~~~~~~~~ ** Message: 00:35:49.112: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.c ** Message: 00:35:49.356: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_score.o] ** Message: 00:35:49.356: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_score.o ** Message: 00:35:49.360: Adding function [optimal_58_ungapped_58_codon_32_find_32_score] ** Message: 00:35:49.360: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path.o] ** Message: 00:35:49.360: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path.o ** Message: 00:35:49.365: Adding function [optimal_58_ungapped_58_codon_32_find_32_path] ** Message: 00:35:49.365: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_region.o] ** Message: 00:35:49.365: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_region.o ** Message: 00:35:49.369: Adding function [optimal_58_ungapped_58_codon_32_find_32_region] ** Message: 00:35:49.369: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_checkpoint.o] ** Message: 00:35:49.369: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_checkpoint.o ** Message: 00:35:49.373: Adding function [optimal_58_ungapped_58_codon_32_find_32_checkpoint] ** Message: 00:35:49.373: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.o] ** Message: 00:35:49.373: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.o ** Message: 00:35:49.378: Adding function [optimal_58_ungapped_58_codon_32_find_32_path_32_continuation] ** Message: 00:35:49.378: Processing model [a:g] ** Message: 00:35:49.378: Bootstrapper processing model [affine:global:dna2dna] ** Message: 00:35:49.378: Process optimal [optimal:affine:global:dna2dna] ** Message: 00:35:49.379: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.c ** Message: 00:35:49.560: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.c ** Message: 00:35:49.813: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.c: In function ‘optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint’: /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.c:33:25: warning: variable ‘transition’ set but not used [-Wunused-but-set-variable] 33 | register C4_Transition *transition; | ^~~~~~~~~~ ** Message: 00:35:50.056: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 00:35:50.338: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.o] ** Message: 00:35:50.338: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.o ** Message: 00:35:50.343: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_score] ** Message: 00:35:50.343: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.o] ** Message: 00:35:50.343: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.o ** Message: 00:35:50.347: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_path] ** Message: 00:35:50.347: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.o] ** Message: 00:35:50.347: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.o ** Message: 00:35:50.351: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint] ** Message: 00:35:50.351: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 00:35:50.351: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 00:35:50.356: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation] ** Message: 00:35:50.356: Bootstrapper processing model [affine:global:protein2protein] ** Message: 00:35:50.356: Process optimal [optimal:affine:global:protein2protein] ** Message: 00:35:50.356: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.c ** Message: 00:35:50.533: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.c ** Message: 00:35:50.777: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.c: In function ‘optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint’: /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.c:33:25: warning: variable ‘transition’ set but not used [-Wunused-but-set-variable] 33 | register C4_Transition *transition; | ^~~~~~~~~~ ** Message: 00:35:51.016: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.c ** Message: 00:35:51.311: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.o] ** Message: 00:35:51.311: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.o ** Message: 00:35:51.315: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_score] ** Message: 00:35:51.315: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.o] ** Message: 00:35:51.315: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.o ** Message: 00:35:51.320: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_path] ** Message: 00:35:51.320: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.o] ** Message: 00:35:51.320: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.o ** Message: 00:35:51.324: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint] ** Message: 00:35:51.324: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.o] ** Message: 00:35:51.324: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.o ** Message: 00:35:51.328: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation] ** Message: 00:35:51.329: Processing model [a:b] ** Message: 00:35:51.329: Bootstrapper processing model [affine:bestfit:dna2dna] ** Message: 00:35:51.329: Process optimal [optimal:affine:bestfit:dna2dna] ** Message: 00:35:51.329: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.c ** Message: 00:35:51.557: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.c ** Message: 00:35:51.889: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.c ** Message: 00:35:52.189: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.c: In function ‘optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint’: /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.c:33:25: warning: variable ‘transition’ set but not used [-Wunused-but-set-variable] 33 | register C4_Transition *transition; | ^~~~~~~~~~ ** Message: 00:35:52.432: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 00:35:52.713: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.o] ** Message: 00:35:52.714: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.o ** Message: 00:35:52.718: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score] ** Message: 00:35:52.718: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.o] ** Message: 00:35:52.718: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.o ** Message: 00:35:52.723: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path] ** Message: 00:35:52.723: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.o] ** Message: 00:35:52.723: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.o ** Message: 00:35:52.727: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region] ** Message: 00:35:52.727: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.o] ** Message: 00:35:52.727: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.o ** Message: 00:35:52.732: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint] ** Message: 00:35:52.732: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 00:35:52.732: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 00:35:52.736: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation] ** Message: 00:35:52.736: Bootstrapper processing model [affine:bestfit:protein2protein] ** Message: 00:35:52.736: Process optimal [optimal:affine:bestfit:protein2protein] ** Message: 00:35:52.737: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.c ** Message: 00:35:52.961: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.c ** Message: 00:35:53.290: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.c ** Message: 00:35:53.591: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.c: In function ‘optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint’: /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.c:33:25: warning: variable ‘transition’ set but not used [-Wunused-but-set-variable] 33 | register C4_Transition *transition; | ^~~~~~~~~~ ** Message: 00:35:53.829: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.c ** Message: 00:35:54.107: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.o] ** Message: 00:35:54.107: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.o ** Message: 00:35:54.112: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score] ** Message: 00:35:54.112: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.o] ** Message: 00:35:54.112: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.o ** Message: 00:35:54.116: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path] ** Message: 00:35:54.116: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.o] ** Message: 00:35:54.116: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.o ** Message: 00:35:54.121: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region] ** Message: 00:35:54.121: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.o] ** Message: 00:35:54.121: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.o ** Message: 00:35:54.126: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint] ** Message: 00:35:54.126: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.o] ** Message: 00:35:54.126: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.o ** Message: 00:35:54.130: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation] ** Message: 00:35:54.131: Processing model [a:l] ** Message: 00:35:54.131: Bootstrapper processing model [affine:local:dna2dna] ** Message: 00:35:54.131: Process optimal [optimal:affine:local:dna2dna] ** Message: 00:35:54.131: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.c ** Message: 00:35:54.242: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.c ** Message: 00:35:54.385: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.c ** Message: 00:35:54.532: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.c: In function ‘optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint’: /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.c:33:25: warning: variable ‘transition’ set but not used [-Wunused-but-set-variable] 33 | register C4_Transition *transition; | ^~~~~~~~~~ ** Message: 00:35:54.776: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 00:35:55.057: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.o] ** Message: 00:35:55.057: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.o ** Message: 00:35:55.062: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_score] ** Message: 00:35:55.062: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.o] ** Message: 00:35:55.062: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.o ** Message: 00:35:55.067: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_path] ** Message: 00:35:55.067: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.o] ** Message: 00:35:55.067: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.o ** Message: 00:35:55.072: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_region] ** Message: 00:35:55.072: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o] ** Message: 00:35:55.072: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o ** Message: 00:35:55.077: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint] ** Message: 00:35:55.077: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 00:35:55.077: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 00:35:55.081: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation] ** Message: 00:35:55.082: Process optimal [Terminal [Segment("START"->"match"):[affine:local:dna2dna]]] ** Message: 00:35:55.083: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:35:55.288: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:35:55.583: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:35:55.583: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:35:55.588: 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: 00:35:55.588: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:35:55.588: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:35:55.592: 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: 00:35:55.592: Process optimal [Terminal [Segment("match"->"END"):[affine:local:dna2dna]]] ** Message: 00:35:55.593: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:35:55.768: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:35:56.006: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:35:56.006: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:35:56.011: 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: 00:35:56.011: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:35:56.011: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:35:56.016: 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: 00:35:56.016: Process optimal [HeuristicJoin:[Segment("match"->"match"):[affine:local:dna2dna]]] ** Message: 00:35:56.017: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:35:56.453: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:35:57.111: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:35:57.111: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:35:57.116: 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: 00:35:57.116: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:35:57.116: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:35:57.121: 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: 00:35:57.121: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.c ** Message: 00:35:57.233: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.c ** Message: 00:35:57.350: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.o] ** Message: 00:35:57.350: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.o ** Message: 00:35:57.355: Adding function [Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded] ** Message: 00:35:57.355: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.o] ** Message: 00:35:57.355: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.o ** Message: 00:35:57.360: Adding function [Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded] ** Message: 00:35:57.360: Bootstrapper processing model [affine:local:protein2protein] ** Message: 00:35:57.360: Process optimal [optimal:affine:local:protein2protein] ** Message: 00:35:57.360: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.c ** Message: 00:35:57.470: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.c ** Message: 00:35:57.609: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.c ** Message: 00:35:57.758: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.c: In function ‘optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint’: /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.c:33:25: warning: variable ‘transition’ set but not used [-Wunused-but-set-variable] 33 | register C4_Transition *transition; | ^~~~~~~~~~ ** Message: 00:35:57.994: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.c ** Message: 00:35:58.271: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.o] ** Message: 00:35:58.271: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.o ** Message: 00:35:58.276: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_score] ** Message: 00:35:58.276: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.o] ** Message: 00:35:58.276: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.o ** Message: 00:35:58.281: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_path] ** Message: 00:35:58.281: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.o] ** Message: 00:35:58.281: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.o ** Message: 00:35:58.286: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_region] ** Message: 00:35:58.286: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o] ** Message: 00:35:58.286: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o ** Message: 00:35:58.291: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint] ** Message: 00:35:58.291: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o] ** Message: 00:35:58.291: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o ** Message: 00:35:58.296: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation] ** Message: 00:35:58.298: Process optimal [Terminal [Segment("START"->"match"):[affine:local:protein2protein]]] ** Message: 00:35:58.298: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:35:58.496: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:35:58.783: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:35:58.783: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:35:58.788: 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: 00:35:58.788: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:35:58.788: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:35:58.793: 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: 00:35:58.793: Process optimal [Terminal [Segment("match"->"END"):[affine:local:protein2protein]]] ** Message: 00:35:58.794: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:35:58.964: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:35:59.192: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:35:59.192: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:35:59.197: 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: 00:35:59.197: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:35:59.197: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:35:59.202: 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: 00:35:59.202: Process optimal [HeuristicJoin:[Segment("match"->"match"):[affine:local:protein2protein]]] ** Message: 00:35:59.203: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:35:59.619: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:00.258: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:00.258: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:00.263: 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: 00:36:00.263: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:00.263: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:00.268: 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: 00:36:00.268: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.c ** Message: 00:36:00.382: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.c ** Message: 00:36:00.498: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.o] ** Message: 00:36:00.498: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.o ** Message: 00:36:00.504: Adding function [Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded] ** Message: 00:36:00.504: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.o] ** Message: 00:36:00.504: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.o ** Message: 00:36:00.509: Adding function [Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded] ** Message: 00:36:00.509: Processing model [a:o] ** Message: 00:36:00.509: Bootstrapper processing model [affine:overlap:dna2dna] ** Message: 00:36:00.509: Process optimal [optimal:affine:overlap:dna2dna] ** Message: 00:36:00.510: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.c ** Message: 00:36:00.705: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.c ** Message: 00:36:00.979: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.c ** Message: 00:36:01.283: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.c: In function ‘optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint’: /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.c:33:25: warning: variable ‘transition’ set but not used [-Wunused-but-set-variable] 33 | register C4_Transition *transition; | ^~~~~~~~~~ ** Message: 00:36:01.525: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 00:36:01.811: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.o] ** Message: 00:36:01.811: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.o ** Message: 00:36:01.816: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score] ** Message: 00:36:01.816: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.o] ** Message: 00:36:01.816: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.o ** Message: 00:36:01.821: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path] ** Message: 00:36:01.821: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.o] ** Message: 00:36:01.821: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.o ** Message: 00:36:01.826: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region] ** Message: 00:36:01.826: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.o] ** Message: 00:36:01.826: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.o ** Message: 00:36:01.831: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint] ** Message: 00:36:01.831: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 00:36:01.831: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 00:36:01.836: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation] ** Message: 00:36:01.836: Processing model [e2g] ** Message: 00:36:01.837: Bootstrapper processing model [est2genome] ** Message: 00:36:01.837: Process optimal [optimal:est2genome] ** Message: 00:36:01.837: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_est2genome_32_find_32_score.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_est2genome_32_find_32_score.c ** Message: 00:36:02.197: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path.c ** Message: 00:36:02.741: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_est2genome_32_find_32_region.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_est2genome_32_find_32_region.c ** Message: 00:36:03.246: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_est2genome_32_find_32_checkpoint.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_est2genome_32_find_32_checkpoint.c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_est2genome_32_find_32_checkpoint.c: In function ‘optimal_58_est2genome_32_find_32_checkpoint’: /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_est2genome_32_find_32_checkpoint.c:35:25: warning: variable ‘transition’ set but not used [-Wunused-but-set-variable] 35 | register C4_Transition *transition; | ^~~~~~~~~~ ** Message: 00:36:04.481: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path_32_continuation.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path_32_continuation.c ** Message: 00:36:06.209: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_est2genome_32_find_32_score.o] ** Message: 00:36:06.209: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_est2genome_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_est2genome_32_find_32_score.o ** Message: 00:36:06.214: Adding function [optimal_58_est2genome_32_find_32_score] ** Message: 00:36:06.214: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path.o] ** Message: 00:36:06.214: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path.o ** Message: 00:36:06.220: Adding function [optimal_58_est2genome_32_find_32_path] ** Message: 00:36:06.220: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_est2genome_32_find_32_region.o] ** Message: 00:36:06.220: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_est2genome_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_est2genome_32_find_32_region.o ** Message: 00:36:06.225: Adding function [optimal_58_est2genome_32_find_32_region] ** Message: 00:36:06.225: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_est2genome_32_find_32_checkpoint.o] ** Message: 00:36:06.225: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_est2genome_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_est2genome_32_find_32_checkpoint.o ** Message: 00:36:06.230: Adding function [optimal_58_est2genome_32_find_32_checkpoint] ** Message: 00:36:06.230: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path_32_continuation.o] ** Message: 00:36:06.230: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path_32_continuation.o ** Message: 00:36:06.236: Adding function [optimal_58_est2genome_32_find_32_path_32_continuation] ** Message: 00:36:06.240: Process optimal [Terminal [Segment("START"->"match reverse"):[est2genome]]] ** Message: 00:36:06.241: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:06.767: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:07.600: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:07.600: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:07.605: 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: 00:36:07.605: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:07.605: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:07.611: 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: 00:36:07.611: Process optimal [Terminal [Segment("match reverse"->"END"):[est2genome]]] ** Message: 00:36:07.611: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:07.936: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:08.401: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:08.401: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:08.407: 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: 00:36:08.407: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:08.407: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:08.413: 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: 00:36:08.413: Process optimal [Terminal [Segment("START"->"match forward"):[est2genome]]] ** Message: 00:36:08.414: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:08.935: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:09.755: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:09.755: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:09.761: 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: 00:36:09.761: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:09.761: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:09.767: 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: 00:36:09.767: Process optimal [Terminal [Segment("match forward"->"END"):[est2genome]]] ** Message: 00:36:09.767: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:10.097: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:10.558: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:10.558: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:10.564: 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: 00:36:10.564: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:10.564: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:10.569: 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: 00:36:10.569: Process optimal [HeuristicJoin:[Segment("match reverse"->"match reverse"):[est2genome]]] ** Message: 00:36:10.571: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:11.612: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:13.367: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:13.367: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:13.372: 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: 00:36:13.372: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:13.372: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:13.378: 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: 00:36:13.378: Process optimal [Src span [Segment("match reverse"->"intron reverse"):[est2genome]]] ** Message: 00:36:13.379: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:13.727: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:14.214: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:14.214: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:14.220: 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: 00:36:14.220: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:14.220: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:14.226: 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: 00:36:14.226: Process optimal [Src span traceback [Segment("match reverse"->"intron reverse"):[est2genome]]] ** Message: 00:36:14.228: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:15.695: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:15.695: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:15.701: 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: 00:36:15.701: Process optimal [Dst span [Segment("intron reverse"->"match reverse"):[est2genome]]] ** Message: 00:36:15.702: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:16.279: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:17.178: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:17.178: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:17.184: 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: 00:36:17.184: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:17.184: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:17.190: 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: 00:36:17.190: Process optimal [HeuristicJoin:[Segment("match forward"->"match forward"):[est2genome]]] ** Message: 00:36:17.193: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:18.254: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:19.987: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:19.987: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:19.993: 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: 00:36:19.993: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:19.993: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:19.999: 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: 00:36:19.999: Process optimal [Src span [Segment("match forward"->"intron forward"):[est2genome]]] ** Message: 00:36:20.000: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:20.344: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:20.823: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:20.823: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:20.830: 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: 00:36:20.830: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:20.830: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:20.836: 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: 00:36:20.836: Process optimal [Src span traceback [Segment("match forward"->"intron forward"):[est2genome]]] ** Message: 00:36:20.837: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:22.248: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:22.248: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:22.255: 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: 00:36:22.255: Process optimal [Dst span [Segment("intron forward"->"match forward"):[est2genome]]] ** Message: 00:36:22.256: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:22.827: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:23.724: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:23.724: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:23.730: 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: 00:36:23.731: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:23.731: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:23.737: 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: 00:36:23.737: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.c: In function ‘Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary’: /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.c:31:21: warning: unused variable ‘shadow’ [-Wunused-variable] 31 | register C4_Shadow *shadow; | ^~~~~~ /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.c:30:30: warning: unused variable ‘span_data’ [-Wunused-variable] 30 | register Scheduler_SpanData *span_data; | ^~~~~~~~~ /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.c:29:20: warning: unused variable ‘span_seed’ [-Wunused-variable] 29 | Scheduler_SpanSeed span_seed; | ^~~~~~~~~ ** Message: 00:36:23.938: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.c ** Message: 00:36:24.152: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.o] ** Message: 00:36:24.153: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.o ** Message: 00:36:24.159: Adding function [Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary] ** Message: 00:36:24.159: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.o] ** Message: 00:36:24.159: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.o ** Message: 00:36:24.165: Adding function [Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary] ** Message: 00:36:24.165: Processing model [ner] ** Message: 00:36:24.166: Bootstrapper processing model [NER:affine:local:dna2dna] ** Message: 00:36:24.166: Process optimal [optimal:NER:affine:local:dna2dna] ** Message: 00:36:24.166: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.c ** Message: 00:36:24.293: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.c ** Message: 00:36:24.459: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.c ** Message: 00:36:24.633: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.c: In function ‘optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint’: /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.c:34:25: warning: variable ‘transition’ set but not used [-Wunused-but-set-variable] 34 | register C4_Transition *transition; | ^~~~~~~~~~ ** Message: 00:36:24.942: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 00:36:25.300: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.o] ** Message: 00:36:25.300: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.o ** Message: 00:36:25.307: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score] ** Message: 00:36:25.307: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.o] ** Message: 00:36:25.307: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.o ** Message: 00:36:25.313: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path] ** Message: 00:36:25.313: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.o] ** Message: 00:36:25.313: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.o ** Message: 00:36:25.320: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region] ** Message: 00:36:25.320: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o] ** Message: 00:36:25.320: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o ** Message: 00:36:25.326: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint] ** Message: 00:36:25.326: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 00:36:25.326: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 00:36:25.333: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation] ** Message: 00:36:25.335: Process optimal [Terminal [Segment("START"->"match"):[NER:affine:local:dna2dna]]] ** Message: 00:36:25.336: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:25.590: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:25.972: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:25.972: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:25.979: 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: 00:36:25.979: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:25.979: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:25.985: 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: 00:36:25.985: Process optimal [Terminal [Segment("match"->"END"):[NER:affine:local:dna2dna]]] ** Message: 00:36:25.986: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:26.195: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:26.493: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:26.493: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:26.500: 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: 00:36:26.500: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:26.500: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:26.506: 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: 00:36:26.506: Process optimal [HeuristicJoin:[Segment("match"->"match"):[NER:affine:local:dna2dna]]] ** Message: 00:36:26.508: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:27.089: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:28.041: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:28.041: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:28.048: 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: 00:36:28.048: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:28.048: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:28.055: 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: 00:36:28.055: Process optimal [Src span [Segment("match"->"ner"):[NER:affine:local:dna2dna]]] ** Message: 00:36:28.055: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:28.286: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:28.609: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:28.609: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:28.616: 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: 00:36:28.616: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:28.616: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:28.622: 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: 00:36:28.622: Process optimal [Src span traceback [Segment("match"->"ner"):[NER:affine:local:dna2dna]]] ** Message: 00:36:28.624: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:29.478: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:29.478: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:29.485: 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: 00:36:29.485: Process optimal [Dst span [Segment("ner"->"match"):[NER:affine:local:dna2dna]]] ** Message: 00:36:29.486: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:29.784: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:30.246: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:30.246: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:30.253: 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: 00:36:30.253: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:30.253: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:30.260: 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: 00:36:30.261: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.c: In function ‘Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary’: /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.c:30:30: warning: unused variable ‘span_data’ [-Wunused-variable] 30 | register Scheduler_SpanData *span_data; | ^~~~~~~~~ /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.c:29:20: warning: unused variable ‘span_seed’ [-Wunused-variable] 29 | Scheduler_SpanSeed span_seed; | ^~~~~~~~~ ** Message: 00:36:30.387: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.c ** Message: 00:36:30.521: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.o] ** Message: 00:36:30.522: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.o ** Message: 00:36:30.528: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary] ** Message: 00:36:30.529: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.o] ** Message: 00:36:30.529: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.o ** Message: 00:36:30.536: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary] ** Message: 00:36:30.536: Bootstrapper processing model [NER:affine:local:protein2protein] ** Message: 00:36:30.536: Process optimal [optimal:NER:affine:local:protein2protein] ** Message: 00:36:30.536: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.c ** Message: 00:36:30.661: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.c ** Message: 00:36:30.825: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.c ** Message: 00:36:30.998: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.c: In function ‘optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint’: /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.c:34:25: warning: variable ‘transition’ set but not used [-Wunused-but-set-variable] 34 | register C4_Transition *transition; | ^~~~~~~~~~ ** Message: 00:36:31.300: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.c ** Message: 00:36:31.660: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.o] ** Message: 00:36:31.660: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.o ** Message: 00:36:31.667: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score] ** Message: 00:36:31.667: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.o] ** Message: 00:36:31.667: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.o ** Message: 00:36:31.674: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path] ** Message: 00:36:31.674: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.o] ** Message: 00:36:31.674: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.o ** Message: 00:36:31.681: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region] ** Message: 00:36:31.681: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o] ** Message: 00:36:31.681: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o ** Message: 00:36:31.688: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint] ** Message: 00:36:31.688: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o] ** Message: 00:36:31.688: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o ** Message: 00:36:31.694: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation] ** Message: 00:36:31.697: Process optimal [Terminal [Segment("START"->"match"):[NER:affine:local:protein2protein]]] ** Message: 00:36:31.697: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:31.944: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:32.325: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:32.325: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:32.332: 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: 00:36:32.332: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:32.332: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:32.339: 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: 00:36:32.339: Process optimal [Terminal [Segment("match"->"END"):[NER:affine:local:protein2protein]]] ** Message: 00:36:32.340: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:32.548: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:32.845: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:32.845: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:32.852: 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: 00:36:32.852: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:32.852: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:32.859: 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: 00:36:32.859: Process optimal [HeuristicJoin:[Segment("match"->"match"):[NER:affine:local:protein2protein]]] ** Message: 00:36:32.860: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:33.421: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:34.336: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:34.336: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:34.343: 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: 00:36:34.343: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:34.343: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:34.350: 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: 00:36:34.350: Process optimal [Src span [Segment("match"->"ner"):[NER:affine:local:protein2protein]]] ** Message: 00:36:34.351: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:34.578: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:34.896: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:34.896: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:34.903: 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: 00:36:34.903: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:34.903: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:34.910: 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: 00:36:34.910: Process optimal [Src span traceback [Segment("match"->"ner"):[NER:affine:local:protein2protein]]] ** Message: 00:36:34.912: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:35.747: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:35.747: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:35.754: 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: 00:36:35.754: Process optimal [Dst span [Segment("ner"->"match"):[NER:affine:local:protein2protein]]] ** Message: 00:36:35.755: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:36.041: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:36.499: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:36.499: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:36.506: 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: 00:36:36.506: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:36.506: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:36.513: 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: 00:36:36.514: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.c: In function ‘Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary’: /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.c:30:30: warning: unused variable ‘span_data’ [-Wunused-variable] 30 | register Scheduler_SpanData *span_data; | ^~~~~~~~~ /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.c:29:20: warning: unused variable ‘span_seed’ [-Wunused-variable] 29 | Scheduler_SpanSeed span_seed; | ^~~~~~~~~ ** Message: 00:36:36.638: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.c ** Message: 00:36:36.773: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.o] ** Message: 00:36:36.773: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.o ** Message: 00:36:36.780: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary] ** Message: 00:36:36.780: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.o] ** Message: 00:36:36.780: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.o ** Message: 00:36:36.787: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary] ** Message: 00:36:36.787: Processing model [p2d] ** Message: 00:36:36.788: Bootstrapper processing model [protein2dna:local] ** Message: 00:36:36.788: Process optimal [optimal:protein2dna:local] ** Message: 00:36:36.788: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_score.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_score.c ** Message: 00:36:36.976: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path.c ** Message: 00:36:37.232: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_region.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_region.c ** Message: 00:36:37.528: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_checkpoint.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_checkpoint.c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_checkpoint.c: In function ‘optimal_58_protein2dna_58_local_32_find_32_checkpoint’: /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_checkpoint.c:35:25: warning: variable ‘transition’ set but not used [-Wunused-but-set-variable] 35 | register C4_Transition *transition; | ^~~~~~~~~~ ** Message: 00:36:38.135: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.c ** Message: 00:36:38.808: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_score.o] ** Message: 00:36:38.808: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_score.o ** Message: 00:36:38.815: Adding function [optimal_58_protein2dna_58_local_32_find_32_score] ** Message: 00:36:38.815: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path.o] ** Message: 00:36:38.815: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path.o ** Message: 00:36:38.823: Adding function [optimal_58_protein2dna_58_local_32_find_32_path] ** Message: 00:36:38.823: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_region.o] ** Message: 00:36:38.823: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_region.o ** Message: 00:36:38.830: Adding function [optimal_58_protein2dna_58_local_32_find_32_region] ** Message: 00:36:38.830: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_checkpoint.o] ** Message: 00:36:38.830: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_checkpoint.o ** Message: 00:36:38.838: Adding function [optimal_58_protein2dna_58_local_32_find_32_checkpoint] ** Message: 00:36:38.838: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.o] ** Message: 00:36:38.838: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.o ** Message: 00:36:38.845: Adding function [optimal_58_protein2dna_58_local_32_find_32_path_32_continuation] ** Message: 00:36:38.849: Process optimal [Terminal [Segment("START"->"match"):[protein2dna:local]]] ** Message: 00:36:38.850: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:39.289: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:40.005: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:40.005: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:40.013: 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: 00:36:40.013: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:40.013: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:40.021: 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: 00:36:40.021: Process optimal [Terminal [Segment("match"->"END"):[protein2dna:local]]] ** Message: 00:36:40.021: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:40.352: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:40.756: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:40.756: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:40.764: 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: 00:36:40.764: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:40.764: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:40.771: 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: 00:36:40.771: Process optimal [HeuristicJoin:[Segment("match"->"match"):[protein2dna:local]]] ** Message: 00:36:40.774: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:41.656: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:43.146: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:43.146: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:43.154: 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: 00:36:43.154: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:43.154: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:43.162: 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: 00:36:43.162: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.c ** Message: 00:36:43.299: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.c ** Message: 00:36:43.439: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.o] ** Message: 00:36:43.439: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.o ** Message: 00:36:43.447: Adding function [Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded] ** Message: 00:36:43.447: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.o] ** Message: 00:36:43.447: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.o ** Message: 00:36:43.454: Adding function [Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded] ** Message: 00:36:43.455: Processing model [p2d:b] ** Message: 00:36:43.455: Bootstrapper processing model [protein2dna:bestfit] ** Message: 00:36:43.455: Process optimal [optimal:protein2dna:bestfit] ** Message: 00:36:43.456: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_score.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_score.c ** Message: 00:36:43.977: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path.c ** Message: 00:36:44.862: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_region.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_region.c ** Message: 00:36:45.672: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.c: In function ‘optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint’: /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.c:35:25: warning: variable ‘transition’ set but not used [-Wunused-but-set-variable] 35 | register C4_Transition *transition; | ^~~~~~~~~~ ** Message: 00:36:46.277: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.c ** Message: 00:36:46.942: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_score.o] ** Message: 00:36:46.942: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_score.o ** Message: 00:36:46.950: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_score] ** Message: 00:36:46.950: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path.o] ** Message: 00:36:46.950: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path.o ** Message: 00:36:46.958: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_path] ** Message: 00:36:46.958: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_region.o] ** Message: 00:36:46.958: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_region.o ** Message: 00:36:46.966: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_region] ** Message: 00:36:46.966: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.o] ** Message: 00:36:46.966: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.o ** Message: 00:36:46.974: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint] ** Message: 00:36:46.974: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.o] ** Message: 00:36:46.974: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.o ** Message: 00:36:46.982: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation] ** Message: 00:36:46.982: Processing model [p2g] ** Message: 00:36:46.982: Bootstrapper processing model [protein2genome:local] ** Message: 00:36:46.982: Process optimal [optimal:protein2genome:local] ** Message: 00:36:46.983: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_score.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_score.c ** Message: 00:36:47.466: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path.c ** Message: 00:36:48.223: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_region.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_region.c ** Message: 00:36:48.889: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_checkpoint.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_checkpoint.c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_checkpoint.c: In function ‘optimal_58_protein2genome_58_local_32_find_32_checkpoint’: /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_checkpoint.c:35:25: warning: variable ‘transition’ set but not used [-Wunused-but-set-variable] 35 | register C4_Transition *transition; | ^~~~~~~~~~ ** Message: 00:36:50.876: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.c ** Message: 00:36:53.782: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_score.o] ** Message: 00:36:53.782: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_score.o ** Message: 00:36:53.790: Adding function [optimal_58_protein2genome_58_local_32_find_32_score] ** Message: 00:36:53.790: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path.o] ** Message: 00:36:53.790: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path.o ** Message: 00:36:53.798: Adding function [optimal_58_protein2genome_58_local_32_find_32_path] ** Message: 00:36:53.798: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_region.o] ** Message: 00:36:53.798: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_region.o ** Message: 00:36:53.806: Adding function [optimal_58_protein2genome_58_local_32_find_32_region] ** Message: 00:36:53.806: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_checkpoint.o] ** Message: 00:36:53.806: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_checkpoint.o ** Message: 00:36:53.814: Adding function [optimal_58_protein2genome_58_local_32_find_32_checkpoint] ** Message: 00:36:53.814: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.o] ** Message: 00:36:53.814: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.o ** Message: 00:36:53.823: Adding function [optimal_58_protein2genome_58_local_32_find_32_path_32_continuation] ** Message: 00:36:53.839: Process optimal [Terminal [Segment("START"->"match"):[protein2genome:local]]] ** Message: 00:36:53.842: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:55.685: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:59.215: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:59.215: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:59.223: 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: 00:36:59.223: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:59.223: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:36:59.232: 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: 00:36:59.232: Process optimal [Terminal [Segment("match"->"END"):[protein2genome:local]]] ** Message: 00:36:59.233: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:37:00.125: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:37:01.595: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:37:01.596: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:37:01.604: 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: 00:37:01.604: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:37:01.604: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:37:01.612: 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: 00:37:01.612: Process optimal [HeuristicJoin:[Segment("match"->"match"):[protein2genome:local]]] ** Message: 00:37:01.617: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:37:05.990: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:37:14.817: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:37:14.817: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:37:14.826: 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: 00:37:14.826: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:37:14.826: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:37:14.835: 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: 00:37:14.835: Process optimal [Src span [Segment("match"->"intron 0:0 phase-T"):[protein2genome:local]]] ** Message: 00:37:14.837: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:37:15.742: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:37:17.253: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:37:17.253: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:37:17.261: 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: 00:37:17.261: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:37:17.261: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:37:17.270: 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: 00:37:17.270: Process optimal [Src span traceback [Segment("match"->"intron 0:0 phase-T"):[protein2genome:local]]] ** Message: 00:37:17.275: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:37:24.519: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:37:24.519: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:37:24.528: 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: 00:37:24.528: Process optimal [Dst span [Segment("intron 0:0 phase-T"->"match"):[protein2genome:local]]] ** Message: 00:37:24.531: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:37:26.475: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:37:30.291: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:37:30.291: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:37:30.300: 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: 00:37:30.300: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:37:30.300: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:37:30.310: 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: 00:37:30.310: Process optimal [Src span [Segment("match"->"intron 1:2 phase-T"):[protein2genome:local]]] ** Message: 00:37:30.311: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:37:31.234: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:37:32.769: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:37:32.769: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:37:32.778: 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: 00:37:32.779: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:37:32.779: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:37:32.788: 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: 00:37:32.788: Process optimal [Src span traceback [Segment("match"->"intron 1:2 phase-T"):[protein2genome:local]]] ** Message: 00:37:32.792: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:37:39.930: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:37:39.930: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:37:39.939: 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: 00:37:39.939: Process optimal [Dst span [Segment("intron 1:2 phase-T"->"match"):[protein2genome:local]]] ** Message: 00:37:39.942: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:37:41.905: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:37:45.674: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:37:45.674: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:37:45.684: 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: 00:37:45.684: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:37:45.684: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:37:45.693: 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: 00:37:45.693: Process optimal [Src span [Segment("match"->"intron 2:1 phase-T"):[protein2genome:local]]] ** Message: 00:37:45.695: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:37:46.611: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:37:48.132: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:37:48.132: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:37:48.141: 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: 00:37:48.142: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:37:48.142: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:37:48.152: 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: 00:37:48.152: Process optimal [Src span traceback [Segment("match"->"intron 2:1 phase-T"):[protein2genome:local]]] ** Message: 00:37:48.156: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:37:55.351: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:37:55.352: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:37:55.362: 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: 00:37:55.362: Process optimal [Dst span [Segment("intron 2:1 phase-T"->"match"):[protein2genome:local]]] ** Message: 00:37:55.364: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:37:57.347: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:38:01.160: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:38:01.160: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:38:01.171: 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: 00:38:01.171: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:38:01.171: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:38:01.182: 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: 00:38:01.182: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.c: In function ‘Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary’: /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.c:30:21: warning: unused variable ‘shadow’ [-Wunused-variable] 30 | register C4_Shadow *shadow; | ^~~~~~ /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.c:29:30: warning: unused variable ‘span_data’ [-Wunused-variable] 29 | register Scheduler_SpanData *span_data; | ^~~~~~~~~ /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.c:28:20: warning: unused variable ‘span_seed’ [-Wunused-variable] 28 | Scheduler_SpanSeed span_seed; | ^~~~~~~~~ ** Message: 00:38:01.378: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.c ** Message: 00:38:01.604: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.o] ** Message: 00:38:01.604: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.o ** Message: 00:38:01.614: Adding function [Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary] ** Message: 00:38:01.615: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.o] ** Message: 00:38:01.615: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.o ** Message: 00:38:01.625: Adding function [Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary] ** Message: 00:38:01.625: Processing model [p2g:b] ** Message: 00:38:01.625: Bootstrapper processing model [protein2genome:bestfit] ** Message: 00:38:01.625: Process optimal [optimal:protein2genome:bestfit] ** Message: 00:38:01.628: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_score.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_score.c ** Message: 00:38:03.956: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path.c ** Message: 00:38:08.505: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_region.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_region.c ** Message: 00:38:11.567: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.c: In function ‘optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint’: /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.c:35:25: warning: variable ‘transition’ set but not used [-Wunused-but-set-variable] 35 | register C4_Transition *transition; | ^~~~~~~~~~ ** Message: 00:38:13.538: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.c ** Message: 00:38:16.462: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_score.o] ** Message: 00:38:16.462: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_score.o ** Message: 00:38:16.473: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_score] ** Message: 00:38:16.473: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path.o] ** Message: 00:38:16.473: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path.o ** Message: 00:38:16.483: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_path] ** Message: 00:38:16.483: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_region.o] ** Message: 00:38:16.483: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_region.o ** Message: 00:38:16.494: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_region] ** Message: 00:38:16.494: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.o] ** Message: 00:38:16.494: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.o ** Message: 00:38:16.505: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint] ** Message: 00:38:16.505: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.o] ** Message: 00:38:16.505: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.o ** Message: 00:38:16.516: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation] ** Message: 00:38:16.516: Processing model [c2c] ** Message: 00:38:16.517: Bootstrapper processing model [coding2coding] ** Message: 00:38:16.517: Process optimal [optimal:coding2coding] ** Message: 00:38:16.518: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_score.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_score.c ** Message: 00:38:16.890: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path.c ** Message: 00:38:17.510: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_region.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_region.c ** Message: 00:38:18.237: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_checkpoint.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_checkpoint.c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_checkpoint.c: In function ‘optimal_58_coding2coding_32_find_32_checkpoint’: /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_checkpoint.c:35:25: warning: variable ‘transition’ set but not used [-Wunused-but-set-variable] 35 | register C4_Transition *transition; | ^~~~~~~~~~ ** Message: 00:38:19.935: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path_32_continuation.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path_32_continuation.c ** Message: 00:38:22.230: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_score.o] ** Message: 00:38:22.230: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_score.o ** Message: 00:38:22.241: Adding function [optimal_58_coding2coding_32_find_32_score] ** Message: 00:38:22.241: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path.o] ** Message: 00:38:22.241: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path.o ** Message: 00:38:22.252: Adding function [optimal_58_coding2coding_32_find_32_path] ** Message: 00:38:22.252: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_region.o] ** Message: 00:38:22.252: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_region.o ** Message: 00:38:22.264: Adding function [optimal_58_coding2coding_32_find_32_region] ** Message: 00:38:22.264: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_checkpoint.o] ** Message: 00:38:22.264: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_checkpoint.o ** Message: 00:38:22.275: Adding function [optimal_58_coding2coding_32_find_32_checkpoint] ** Message: 00:38:22.275: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path_32_continuation.o] ** Message: 00:38:22.275: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path_32_continuation.o ** Message: 00:38:22.286: Adding function [optimal_58_coding2coding_32_find_32_path_32_continuation] ** Message: 00:38:22.301: Process optimal [Terminal [Segment("START"->"match"):[coding2coding]]] ** Message: 00:38:22.304: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:38:23.514: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:38:25.804: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:38:25.804: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:38:25.815: 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: 00:38:25.815: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:38:25.816: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:38:25.827: 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: 00:38:25.827: Process optimal [Terminal [Segment("match"->"END"):[coding2coding]]] ** Message: 00:38:25.828: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:38:26.415: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:38:27.368: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:38:27.368: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:38:27.380: 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: 00:38:27.380: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:38:27.380: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:38:27.391: 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: 00:38:27.392: Process optimal [HeuristicJoin:[Segment("match"->"match"):[coding2coding]]] ** Message: 00:38:27.395: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:38:30.109: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:38:35.169: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:38:35.169: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:38:35.181: 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: 00:38:35.181: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:38:35.181: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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 /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/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: 00:38:35.192: 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: 00:38:35.193: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.c ** Message: 00:38:35.354: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.c ** Message: 00:38:35.521: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.o] ** Message: 00:38:35.521: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.o ** Message: 00:38:35.533: Adding function [Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded] ** Message: 00:38:35.533: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.o] ** Message: 00:38:35.533: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.o ** Message: 00:38:35.545: Adding function [Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded] ** Message: 00:38:35.545: Processing model [c2g] ** Message: 00:38:35.546: Bootstrapper processing model [coding2genome] ** Message: 00:38:35.546: Process optimal [optimal:coding2genome] ** Message: 00:38:35.547: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_score.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_score.c ** Message: 00:38:36.748: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path.c ** Message: 00:38:38.914: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_region.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_region.c ** Message: 00:38:40.745: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_checkpoint.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_checkpoint.c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_checkpoint.c: In function ‘optimal_58_coding2genome_32_find_32_checkpoint’: /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_checkpoint.c:35:25: warning: variable ‘transition’ set but not used [-Wunused-but-set-variable] 35 | register C4_Transition *transition; | ^~~~~~~~~~ ** Message: 00:38:48.084: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path_32_continuation.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path_32_continuation.c ** Message: 00:38:59.874: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_score.o] ** Message: 00:38:59.874: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_score.o ** Message: 00:38:59.887: Adding function [optimal_58_coding2genome_32_find_32_score] ** Message: 00:38:59.887: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path.o] ** Message: 00:38:59.887: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path.o ** Message: 00:38:59.899: Adding function [optimal_58_coding2genome_32_find_32_path] ** Message: 00:38:59.899: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_region.o] ** Message: 00:38:59.899: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_region.o ** Message: 00:38:59.911: Adding function [optimal_58_coding2genome_32_find_32_region] ** Message: 00:38:59.911: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_checkpoint.o] ** Message: 00:38:59.911: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_checkpoint.o ** Message: 00:38:59.923: Adding function [optimal_58_coding2genome_32_find_32_checkpoint] ** Message: 00:38:59.923: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path_32_continuation.o] ** Message: 00:38:59.923: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path_32_continuation.o ** Message: 00:38:59.935: Adding function [optimal_58_coding2genome_32_find_32_path_32_continuation] ** Message: 00:38:59.936: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.c: In function ‘Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary’: /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.c:30:21: warning: unused variable ‘shadow’ [-Wunused-variable] 30 | register C4_Shadow *shadow; | ^~~~~~ /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.c:29:30: warning: unused variable ‘span_data’ [-Wunused-variable] 29 | register Scheduler_SpanData *span_data; | ^~~~~~~~~ /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.c:28:20: warning: unused variable ‘span_seed’ [-Wunused-variable] 28 | Scheduler_SpanSeed span_seed; | ^~~~~~~~~ ** Message: 00:39:00.160: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.c ** Message: 00:39:00.419: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.o] ** Message: 00:39:00.420: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.o ** Message: 00:39:00.432: Adding function [Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary] ** Message: 00:39:00.432: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.o] ** Message: 00:39:00.432: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.o ** Message: 00:39:00.444: Adding function [Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary] ** Message: 00:39:00.444: Processing model [cd2g] ** Message: 00:39:00.445: Bootstrapper processing model [cdna2genome] ** Message: 00:39:00.445: Process optimal [optimal:cdna2genome] ** Message: 00:39:00.448: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_score.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_score.c ** Message: 00:39:03.899: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path.c ** Message: 00:39:10.757: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_region.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_region.c ** Message: 00:39:16.230: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_checkpoint.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_checkpoint.c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_checkpoint.c: In function ‘optimal_58_cdna2genome_32_find_32_checkpoint’: /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_checkpoint.c:35:25: warning: variable ‘transition’ set but not used [-Wunused-but-set-variable] 35 | register C4_Transition *transition; | ^~~~~~~~~~ ** Message: 00:39:44.300: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path_32_continuation.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path_32_continuation.c ** Message: 00:40:32.111: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_score.o] ** Message: 00:40:32.111: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_score.o ** Message: 00:40:32.123: Adding function [optimal_58_cdna2genome_32_find_32_score] ** Message: 00:40:32.123: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path.o] ** Message: 00:40:32.123: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path.o ** Message: 00:40:32.136: Adding function [optimal_58_cdna2genome_32_find_32_path] ** Message: 00:40:32.136: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_region.o] ** Message: 00:40:32.136: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_region.o ** Message: 00:40:32.149: Adding function [optimal_58_cdna2genome_32_find_32_region] ** Message: 00:40:32.149: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_checkpoint.o] ** Message: 00:40:32.149: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_checkpoint.o ** Message: 00:40:32.162: Adding function [optimal_58_cdna2genome_32_find_32_checkpoint] ** Message: 00:40:32.162: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path_32_continuation.o] ** Message: 00:40:32.162: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path_32_continuation.o ** Message: 00:40:32.176: Adding function [optimal_58_cdna2genome_32_find_32_path_32_continuation] ** Message: 00:40:32.177: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.c: In function ‘Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary’: /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.c:30:21: warning: unused variable ‘shadow’ [-Wunused-variable] 30 | register C4_Shadow *shadow; | ^~~~~~ /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.c:29:30: warning: unused variable ‘span_data’ [-Wunused-variable] 29 | register Scheduler_SpanData *span_data; | ^~~~~~~~~ /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.c:28:20: warning: unused variable ‘span_seed’ [-Wunused-variable] 28 | Scheduler_SpanSeed span_seed; | ^~~~~~~~~ ** Message: 00:40:32.557: Compiling codegen: gcc -O2 -Wall -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp -o /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o -c /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.c ** Message: 00:40:32.998: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o] ** Message: 00:40:32.998: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o ** Message: 00:40:33.011: Adding function [Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary] ** Message: 00:40:33.011: Adding: [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o] ** Message: 00:40:33.011: Adding object file [/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/codegen/i586_45_slackware_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o ** Message: 00:40:33.025: Adding function [Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary] ** Message: 00:40:33.025: Compiling with: [gcc -O2 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4 -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general -I/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -o c4_model_lookup.o -c c4_model_lookup.c] ** Message: 00:40:33.172: Adding: [c4_model_lookup.o] ** Message: 00:40:33.172: Adding object file [c4_model_lookup.o] to archive ar -Sq c4_model_archive.a c4_model_lookup.o ** Message: 00:40:33.185: Indexing archive [c4_model_archive.a] ranlib c4_model_archive.a ** Message: 00:40:33.207: Done ** Message: 00:40:33.207: Finished building bootstrapping components gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/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="\"i586-slackware-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I. \ -DUSE_COMPILED_MODELS \ -c ../../src/c4/viterbi.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/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="\"i586-slackware-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I. \ -DUSE_COMPILED_MODELS \ -c ../../src/sdp/scheduler.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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="\"i586-slackware-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/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] 264 | g_strup(primer_a); | ^~~~~~~ In file included from /usr/include/glib-2.0/glib.h:82, from ipcress.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here 210 | gchar* g_strup (gchar *string); | ^~~~~~~ ipcress.c:265:9: warning: ‘g_strup’ is deprecated [-Wdeprecated-declarations] 265 | g_strup(primer_b); | ^~~~~~~ In file included from /usr/include/glib-2.0/glib.h:82, from ipcress.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here 210 | gchar* g_strup (gchar *string); | ^~~~~~~ gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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="\"i586-slackware-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c exonerate-server.c exonerate-server.c: In function ‘Exonerate_Server_get_hsps’: exonerate-server.c:349:13: warning: Deprecated pre-processor symbol: replace with "g_string_append_printf" 349 | g_string_sprintfa(str, "hspset: %d", index_hsp_set->target_id); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ exonerate-server.c:354:13: warning: Deprecated pre-processor symbol: replace with "g_string_append_printf" 354 | g_string_sprintfa(str, " %d %d %d", | ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ exonerate-server.c:357:13: warning: Deprecated pre-processor symbol: replace with "g_string_append_printf" 357 | g_string_sprintfa(str, "\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 make[2]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/program' Making all in util make[2]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/util' gcc -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 -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastaclean.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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 -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastaclip.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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 -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastachecksum.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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 -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastacomposition.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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 -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/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] 70 | comp = g_strcasecmp; | ^~~~ In file included from /usr/include/glib-2.0/glib.h:82, from ../../src/general/argument.h:26, from fastadiff.c:19: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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 -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastaexplode.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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 -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/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] 121 | if(!g_strcasecmp(query, "stdin")){ | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from ../../src/general/argument.h:26, from fastafetch.c:21: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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 -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastahardmask.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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 -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastaindex.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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 -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastalength.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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 -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastanrdb.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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 -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastaoverlap.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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 -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastareformat.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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 -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/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] 73 | if(!g_strcasecmp(remove_path, "stdin")){ | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from ../../src/general/argument.h:26, from fastaremove.c:19: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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 -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastarevcomp.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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 -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastasoftmask.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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 -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/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] 130 | if(!g_strcasecmp(sort_key, "id")) | ^~ In file included from /usr/include/glib-2.0/glib.h:82, from ../../src/general/argument.h:26, from fastasort.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ fastasort.c:132:5: warning: ‘g_strcasecmp’ is deprecated [-Wdeprecated-declarations] 132 | else if(!g_strcasecmp(sort_key, "len")) | ^~~~ In file included from /usr/include/glib-2.0/glib.h:82, from ../../src/general/argument.h:26, from fastasort.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ fastasort.c:134:5: warning: ‘g_strcasecmp’ is deprecated [-Wdeprecated-declarations] 134 | else if(!g_strcasecmp(sort_key, "seq")) | ^~~~ In file included from /usr/include/glib-2.0/glib.h:82, from ../../src/general/argument.h:26, from fastasort.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here 201 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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 -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/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] 92 | output_dir, G_DIR_SEPARATOR, g_basename(query_path)); | ^~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:48, from ../../src/general/argument.h:26, from fastasplit.c:20: /usr/include/glib-2.0/glib/gfileutils.h:205:14: note: declared here 205 | const gchar *g_basename (const gchar *file_name); | ^~~~~~~~~~ gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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 -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastasubseq.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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 -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastatranslate.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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 -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastavalidcds.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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 -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fasta2esd.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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 -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastaannotatecdna.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 gcc -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 -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c esd2esi.c gcc -O2 -march=i586 -mtune=i686 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -lgthread-2.0 -pthread -lglib-2.0 -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 -lglib-2.0 make[2]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/util' make[2]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src' make[2]: Nothing to be done for 'all-am'. make[2]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src' make[1]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src' Making all in test make[1]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/test' Making all in data make[2]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/test/data' Making all in cdna make[3]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/test/data/cdna' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/test/data/cdna' Making all in protein make[3]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/test/data/protein' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/test/data/protein' make[3]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/test/data' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/test/data' make[2]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/test/data' Making all in exonerate make[2]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/test/exonerate' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/test/exonerate' Making all in ipcress make[2]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/test/ipcress' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/test/ipcress' Making all in util make[2]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/test/util' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/test/util' make[2]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/test' make[2]: Nothing to be done for 'all-am'. make[2]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/test' make[1]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/test' make[1]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0' make[1]: Nothing to be done for 'all-am'. make[1]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0' Making install in doc make[1]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/doc' Making install in man make[2]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/doc/man' Making install in man1 make[3]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/doc/man/man1' make[4]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/doc/man/man1' make[4]: Nothing to be done for 'install-exec-am'. make install-man1 make[5]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/doc/man/man1' /bin/sh ../../../mkinstalldirs /usr/src/slapt-src/academic/exonerate/package-exonerate/usr/man/man1 mkdir /usr/src/slapt-src/academic/exonerate/package-exonerate/usr mkdir /usr/src/slapt-src/academic/exonerate/package-exonerate/usr/man mkdir /usr/src/slapt-src/academic/exonerate/package-exonerate/usr/man/man1 /usr/bin/ginstall -c -m 644 ./exonerate.1 /usr/src/slapt-src/academic/exonerate/package-exonerate/usr/man/man1/exonerate.1 /usr/bin/ginstall -c -m 644 ./ipcress.1 /usr/src/slapt-src/academic/exonerate/package-exonerate/usr/man/man1/ipcress.1 /usr/bin/ginstall -c -m 644 ./exonerate-server.1 /usr/src/slapt-src/academic/exonerate/package-exonerate/usr/man/man1/exonerate-server.1 /usr/bin/ginstall -c -m 644 ./fastautils.1 /usr/src/slapt-src/academic/exonerate/package-exonerate/usr/man/man1/fastautils.1 make[5]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/doc/man/man1' make[4]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/doc/man/man1' make[3]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/doc/man/man1' make[3]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/doc/man' make[4]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/doc/man' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/doc/man' make[3]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/doc/man' make[2]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/doc/man' make[2]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/doc' make[3]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/doc' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/doc' make[2]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/doc' make[1]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/doc' Making install in src make[1]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src' Making install in struct make[2]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct' make[3]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct' make[2]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/struct' Making install in general make[2]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general' make[3]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general' make[2]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/general' Making install in sequence make[2]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence' make[3]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence' make[2]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sequence' Making install in comparison make[2]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison' make[3]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison' make[2]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/comparison' Making install in database make[2]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/database' make[3]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/database' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/database' make[2]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/database' Making install in c4 make[2]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4' make[3]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4' make[2]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/c4' Making install in bsdp make[2]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp' make[3]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp' make[2]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/bsdp' Making install in sdp make[2]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp' make[3]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp' make[2]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/sdp' Making install in model make[2]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model' make[3]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model' make[2]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/model' Making install in hub make[2]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/hub' make[3]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/hub' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/hub' make[2]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/hub' Making install in program make[2]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/program' make[3]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/program' /bin/sh ../../mkinstalldirs /usr/src/slapt-src/academic/exonerate/package-exonerate/usr/bin mkdir /usr/src/slapt-src/academic/exonerate/package-exonerate/usr/bin /usr/bin/ginstall -c exonerate /usr/src/slapt-src/academic/exonerate/package-exonerate/usr/bin/exonerate /usr/bin/ginstall -c ipcress /usr/src/slapt-src/academic/exonerate/package-exonerate/usr/bin/ipcress /usr/bin/ginstall -c exonerate-server /usr/src/slapt-src/academic/exonerate/package-exonerate/usr/bin/exonerate-server make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/program' make[2]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/program' Making install in util make[2]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/util' make[3]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/util' /bin/sh ../../mkinstalldirs /usr/src/slapt-src/academic/exonerate/package-exonerate/usr/bin /usr/bin/ginstall -c fastaclean /usr/src/slapt-src/academic/exonerate/package-exonerate/usr/bin/fastaclean /usr/bin/ginstall -c fastaclip /usr/src/slapt-src/academic/exonerate/package-exonerate/usr/bin/fastaclip /usr/bin/ginstall -c fastachecksum /usr/src/slapt-src/academic/exonerate/package-exonerate/usr/bin/fastachecksum /usr/bin/ginstall -c fastacomposition /usr/src/slapt-src/academic/exonerate/package-exonerate/usr/bin/fastacomposition /usr/bin/ginstall -c fastadiff /usr/src/slapt-src/academic/exonerate/package-exonerate/usr/bin/fastadiff /usr/bin/ginstall -c fastaexplode /usr/src/slapt-src/academic/exonerate/package-exonerate/usr/bin/fastaexplode /usr/bin/ginstall -c fastafetch /usr/src/slapt-src/academic/exonerate/package-exonerate/usr/bin/fastafetch /usr/bin/ginstall -c fastahardmask /usr/src/slapt-src/academic/exonerate/package-exonerate/usr/bin/fastahardmask /usr/bin/ginstall -c fastaindex /usr/src/slapt-src/academic/exonerate/package-exonerate/usr/bin/fastaindex /usr/bin/ginstall -c fastalength /usr/src/slapt-src/academic/exonerate/package-exonerate/usr/bin/fastalength /usr/bin/ginstall -c fastanrdb /usr/src/slapt-src/academic/exonerate/package-exonerate/usr/bin/fastanrdb /usr/bin/ginstall -c fastaoverlap /usr/src/slapt-src/academic/exonerate/package-exonerate/usr/bin/fastaoverlap /usr/bin/ginstall -c fastareformat /usr/src/slapt-src/academic/exonerate/package-exonerate/usr/bin/fastareformat /usr/bin/ginstall -c fastaremove /usr/src/slapt-src/academic/exonerate/package-exonerate/usr/bin/fastaremove /usr/bin/ginstall -c fastarevcomp /usr/src/slapt-src/academic/exonerate/package-exonerate/usr/bin/fastarevcomp /usr/bin/ginstall -c fastasoftmask /usr/src/slapt-src/academic/exonerate/package-exonerate/usr/bin/fastasoftmask /usr/bin/ginstall -c fastasort /usr/src/slapt-src/academic/exonerate/package-exonerate/usr/bin/fastasort /usr/bin/ginstall -c fastasplit /usr/src/slapt-src/academic/exonerate/package-exonerate/usr/bin/fastasplit /usr/bin/ginstall -c fastasubseq /usr/src/slapt-src/academic/exonerate/package-exonerate/usr/bin/fastasubseq /usr/bin/ginstall -c fastatranslate /usr/src/slapt-src/academic/exonerate/package-exonerate/usr/bin/fastatranslate /usr/bin/ginstall -c fastavalidcds /usr/src/slapt-src/academic/exonerate/package-exonerate/usr/bin/fastavalidcds /usr/bin/ginstall -c fasta2esd /usr/src/slapt-src/academic/exonerate/package-exonerate/usr/bin/fasta2esd /usr/bin/ginstall -c fastaannotatecdna /usr/src/slapt-src/academic/exonerate/package-exonerate/usr/bin/fastaannotatecdna /usr/bin/ginstall -c esd2esi /usr/src/slapt-src/academic/exonerate/package-exonerate/usr/bin/esd2esi make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/util' make[2]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src/util' make[2]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src' make[3]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src' make[2]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src' make[1]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/src' Making install in test make[1]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/test' Making install in data make[2]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/test/data' Making install in cdna make[3]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/test/data/cdna' make[4]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/test/data/cdna' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/test/data/cdna' make[3]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/test/data/cdna' Making install in protein make[3]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/test/data/protein' make[4]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/test/data/protein' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/test/data/protein' make[3]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/test/data/protein' make[3]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/test/data' make[4]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/test/data' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/test/data' make[3]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/test/data' make[2]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/test/data' Making install in exonerate make[2]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/test/exonerate' make[3]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/test/exonerate' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/test/exonerate' make[2]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/test/exonerate' Making install in ipcress make[2]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/test/ipcress' make[3]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/test/ipcress' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/test/ipcress' make[2]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/test/ipcress' Making install in util make[2]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/test/util' make[3]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/test/util' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/test/util' make[2]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/test/util' make[2]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/test' make[3]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/test' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/test' make[2]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/test' make[1]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0/test' make[1]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0' make[2]: Entering directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0' make[2]: Nothing to be done for 'install-exec-am'. make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0' make[1]: Leaving directory '/usr/src/slapt-src/academic/exonerate/exonerate-2.4.0' Slackware package maker, version 3.14159265. Searching for symbolic links: No symbolic links were found, so we won't make an installation script. You can make your own later in ./install/doinst.sh and rebuild the package if you like. This next step is optional - you can set the directories in your package to some sane permissions. If any of the directories in your package have special permissions, then DO NOT reset them here! Would you like to reset all directory permissions to 755 (drwxr-xr-x) and directory ownerships to root.root ([y]es, [n]o)? n Creating Slackware package: /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0-i586-1salix15.0.txz ./ install/ install/slack-desc usr/ usr/bin/ usr/bin/esd2esi usr/bin/exonerate usr/bin/exonerate-server usr/bin/fasta2esd usr/bin/fastaannotatecdna usr/bin/fastachecksum usr/bin/fastaclean usr/bin/fastaclip usr/bin/fastacomposition usr/bin/fastadiff usr/bin/fastaexplode usr/bin/fastafetch usr/bin/fastahardmask usr/bin/fastaindex usr/bin/fastalength usr/bin/fastanrdb usr/bin/fastaoverlap usr/bin/fastareformat usr/bin/fastaremove usr/bin/fastarevcomp usr/bin/fastasoftmask usr/bin/fastasort usr/bin/fastasplit usr/bin/fastasubseq usr/bin/fastatranslate usr/bin/fastavalidcds usr/bin/ipcress usr/doc/ usr/doc/exonerate-2.4.0/ usr/doc/exonerate-2.4.0/AUTHORS usr/doc/exonerate-2.4.0/ChangeLog usr/doc/exonerate-2.4.0/INSTALL usr/doc/exonerate-2.4.0/README usr/doc/exonerate-2.4.0/TODO usr/doc/exonerate-2.4.0/exonerate.SlackBuild usr/man/ usr/man/man1/ usr/man/man1/exonerate-server.1.gz usr/man/man1/exonerate.1.gz usr/man/man1/fastautils.1.gz usr/man/man1/ipcress.1.gz Slackware package /usr/src/slapt-src/academic/exonerate/exonerate-2.4.0-i586-1salix15.0.txz created. Installing package exonerate-2.4.0-i586-1salix15.0... | exonerate (A generic tool for sequence alignment) | | Exonerate is a generic tool for pairwise sequence comparison. | It allows you to align sequences using a many alignment models, | either exhaustive dynamic programming or a variety of heuristics. | | https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate | | | | | |