------------------------------------------------------------------------------- -- Phase: Environment ------------------------------------------------------------------------------- NO_DEPENDS=1 UNAME_r=6.1 UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=unknown UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 LANG=C HOME=/root USER=root TERM=dumb SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: showconfig ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ENV ------------------------------------------------------------------------------- PKG_CONFIG=pkgconf XDG_DATA_HOME=/construction/biology/exonerate XDG_CONFIG_HOME=/construction/biology/exonerate HOME=/construction/biology/exonerate TMPDIR="/tmp" PATH=/construction/biology/exonerate/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8 CONFIG_SITE=/xports/Templates/config.site lt_cv_sys_max_cmd_len=262144 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ARGS ------------------------------------------------------------------------------- --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ENV ------------------------------------------------------------------------------- XDG_DATA_HOME=/construction/biology/exonerate XDG_CONFIG_HOME=/construction/biology/exonerate HOME=/construction/biology/exonerate TMPDIR="/tmp" PATH=/construction/biology/exonerate/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc80 LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8 PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ARGS ------------------------------------------------------------------------------- DESTDIR=/construction/biology/exonerate/stage SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: PLIST_SUB ------------------------------------------------------------------------------- GTK2_VERSION="2.10.0" GTK3_VERSION="3.0.0" OSREL=6.1 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/exonerate" EXAMPLESDIR="share/examples/exonerate" DATADIR="share/exonerate" WWWDIR="www/exonerate" ETCDIR="etc/exonerate" SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: SUB_LIST ------------------------------------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/exonerate DOCSDIR=/usr/local/share/doc/exonerate EXAMPLESDIR=/usr/local/share/examples/exonerate WWWDIR=/usr/local/www/exonerate ETCDIR=/usr/local/etc/exonerate SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: /etc/make.conf ------------------------------------------------------------------------------- DPORTS_BUILDER=yes DISABLE_LICENSES=yes DEFAULT_VERSIONS=ssl=openssl FORCE_PACKAGE=yes DEVELOPER=yes USE_PACKAGE_DEPENDS_ONLY=yes PORTSDIR=/xports PORT_DBDIR=/options PKG_DBDIR=/var/db/pkg PKG_CACHEDIR=/var/cache/pkg PKG_SUFX=.txz DEVELOPER=1 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=600100 OSVERSION=9999999 OSREL=6.1 _OSRELEASE=6.1-SYNTH DISTDIR=/distfiles WRKDIRPREFIX=/construction BATCH=yes PACKAGE_BUILDING=yes PKG_CREATE_VERBOSE=yes MAKE_JOBS_NUMBER=10 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/pkgconf-1.7.4,1.txz Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/libffi-3.3_1.txz Installing /packages/All/pcre-8.44.txz Installing /packages/All/gettext-runtime-0.21.txz Installing /packages/All/libxml2-2.9.10_3.txz Installing /packages/All/libiconv-1.16.txz Installing /packages/All/expat-2.2.10.txz Installing /packages/All/ncurses-6.2.20210313_1.txz ===== Message from ncurses-6.2.20210313_1: -- { type: install message: < exonerate-2.4.0 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> exonerate-2.4.0 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by exonerate-2.4.0 for building SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> exonerate-2.4.0 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by exonerate-2.4.0 for building => SHA256 Checksum OK for exonerate-2.4.0.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> exonerate-2.4.0 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by exonerate-2.4.0 for building ===> Extracting for exonerate-2.4.0 => SHA256 Checksum OK for exonerate-2.4.0.tar.gz. Extracted Memory Use: 3.43M SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for exonerate-2.4.0 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> exonerate-2.4.0 depends on package: pkgconf>=1.3.0_1 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- ===> exonerate-2.4.0 depends on shared library: libglib-2.0.so - found (/usr/local/lib/libglib-2.0.so) ===> exonerate-2.4.0 depends on shared library: libintl.so - found (/usr/local/lib/libintl.so) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> exonerate-2.4.0 depends on package: pkgconf>=1.3.0_1 - found ===> exonerate-2.4.0 depends on shared library: libglib-2.0.so - found (/usr/local/lib/libglib-2.0.so) ===> exonerate-2.4.0 depends on shared library: libintl.so - found (/usr/local/lib/libintl.so) ===> Configuring for exonerate-2.4.0 configure: loading site script /xports/Templates/config.site checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking whether make sets $(MAKE)... yes checking for working aclocal-1.4... missing checking for working autoconf... missing checking for working automake-1.4... missing checking for working autoheader... missing checking for working makeinfo... missing checking for gcc... cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for a BSD-compatible install... /usr/bin/install -c checking whether make sets $(MAKE)... (cached) yes checking for an ANSI C-conforming const... yes checking for inline... inline checking how to run the C preprocessor... cpp checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep checking for ANSI C header files... (cached) yes checking for sys/types.h... (cached) yes checking for sys/stat.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for memory.h... (cached) yes checking for strings.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for unistd.h... (cached) yes checking for limits.h... (cached) yes checking for errno.h... (cached) yes checking for math.h... (cached) yes checking for strings.h... (cached) yes checking for ctype.h... (cached) yes checking for sys/stat.h... (cached) yes checking for sys/types.h... (cached) yes checking for time.h... (cached) yes checking for unistd.h... (cached) yes checking build system type... x86_64-portbld-dragonfly6.1 checking host system type... x86_64-portbld-dragonfly6.1 Set host to x86_64-portbld-dragonfly6.1 x86_64-portbld-dragonfly6.1 Customising build for X86_64 Set source_root_dir to /construction/biology/exonerate/exonerate-2.4.0 ---------------------------------------------------------------- checking for socklen_t... yes checking for pkg-config... /usr/local/bin/pkg-config Using GLIB-2 Turning assertions off Turning paranoid options off Not using options for profiling with gprof Not using options for analysis with gcov Adding support for LARGE FILES (>2Gb) for a 32 bit system Using COMPILED C4 MODELS Installing UTILITIES Using PTHREADS ---------------------------------------------------------------- configure: creating ./config.status config.status: creating Makefile config.status: creating doc/Makefile config.status: creating doc/man/Makefile config.status: creating doc/man/man1/Makefile config.status: creating src/Makefile config.status: creating src/general/Makefile config.status: creating src/sequence/Makefile config.status: creating src/database/Makefile config.status: creating src/struct/Makefile config.status: creating src/comparison/Makefile config.status: creating src/c4/Makefile config.status: creating src/bsdp/Makefile config.status: creating src/sdp/Makefile config.status: creating src/hub/Makefile config.status: creating src/model/Makefile config.status: creating src/program/Makefile config.status: creating src/util/Makefile config.status: creating test/Makefile config.status: creating test/util/Makefile config.status: creating test/ipcress/Makefile config.status: creating test/exonerate/Makefile config.status: creating test/data/Makefile config.status: creating test/data/cdna/Makefile config.status: creating test/data/protein/Makefile SUCCEEDED 00:00:08 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for exonerate-2.4.0 Making all in doc Making all in man Making all in man1 Making all in src Making all in struct cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fsm.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fsm.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c recyclebin.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fsm.test fsm.test.o fsm.o recyclebin.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c matrix.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c matrix.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o matrix.test matrix.test.o matrix.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c pqueue.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c pqueue.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o pqueue.test pqueue.test.o pqueue.o recyclebin.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c slist.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c slist.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o slist.test slist.test.o slist.o recyclebin.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c rangetree.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c rangetree.c rangetree.c: In function 'RangeTree_insert_recent': rangetree.c:151:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] g_tree_traverse(rt->recent_data, RangeTree_insert_recent_collect, ^~~~~~~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:91, from rangetree.h:23, from rangetree.c:18: /usr/local/include/glib-2.0/glib/gtree.h:88:10: note: declared here void g_tree_traverse (GTree *tree, ^~~~~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o rangetree.test rangetree.test.o rangetree.o recyclebin.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c vfsm.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c vfsm.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o vfsm.test vfsm.test.o vfsm.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c recyclebin.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o recyclebin.test recyclebin.test.o recyclebin.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c sparsecache.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c sparsecache.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o sparsecache.test sparsecache.test.o sparsecache.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c dejavu.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c dejavu.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o dejavu.test dejavu.test.o dejavu.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c bitarray.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c bitarray.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o bitarray.test bitarray.test.o bitarray.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c splaytree.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c splaytree.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o splaytree.test splaytree.test.o splaytree.o recyclebin.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c noitree.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c noitree.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o noitree.test noitree.test.o noitree.o recyclebin.o splaytree.o -L/usr/local/lib -lglib-2.0 -lintl Making all in general cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c argument.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c argument.c argument.c: In function 'ArgumentParse_boolean': argument.c:138:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(arg_string, true_string[i])) ^~ In file included from /usr/local/include/glib-2.0/glib.h:82, from argument.h:26, from argument.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ argument.c:140:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(arg_string, false_string[i])) ^~ In file included from /usr/local/include/glib-2.0/glib.h:82, from argument.h:26, from argument.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ argument.c: In function 'main': argument.c:306:13: warning: Deprecated pre-processor symbol if(!g_thread_supported()) ^~~~~~~~~~~~~~~~~ argument.c:307:9: warning: 'g_thread_init' is deprecated [-Wdeprecated-declarations] g_thread_init(NULL); ^~~~~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:111, from argument.h:26, from argument.c:16: /usr/local/include/glib-2.0/glib/deprecated/gthread.h:261:10: note: declared here void g_thread_init (gpointer vtable); ^~~~~~~~~~~~~ argument.c: In function 'Argument_process': argument.c:502:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] g_tree_traverse(arg->option_registry, Argument_set_env_var_func, ^~~~~~~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:91, from argument.h:26, from argument.c:16: /usr/local/include/glib-2.0/glib/gtree.h:88:10: note: declared here void g_tree_traverse (GTree *tree, ^~~~~~~~~~~~~~~ argument.c:559:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] g_tree_traverse(arg->option_registry, ^~~~~~~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:91, from argument.h:26, from argument.c:16: /usr/local/include/glib-2.0/glib/gtree.h:88:10: note: declared here void g_tree_traverse (GTree *tree, ^~~~~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o argument.test argument.test.o argument.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c lineparse.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c lineparse.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o lineparse.test lineparse.test.o lineparse.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c compoundfile.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c compoundfile.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o compoundfile.test compoundfile.test.o compoundfile.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c socket.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c socket.c socket.c: In function 'Socket_send': socket.c:168:13: warning: Deprecated pre-processor symbol, replace with g_string_sprintfa(full_msg, "linecount: %d\n", line_count+1); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ socket.c:169:13: warning: Deprecated pre-processor symbol, replace with g_string_sprintfa(full_msg, "%s", msg); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o socket.test socket.test.o socket.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c jobqueue.test.c jobqueue.test.c: In function 'main': jobqueue.test.c:34:13: warning: Deprecated pre-processor symbol if(!g_thread_supported()) ^~~~~~~~~~~~~~~~~ jobqueue.test.c:35:9: warning: 'g_thread_init' is deprecated [-Wdeprecated-declarations] g_thread_init(NULL); ^~~~~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:111, from jobqueue.h:23, from jobqueue.test.c:17: /usr/local/include/glib-2.0/glib/deprecated/gthread.h:261:10: note: declared here void g_thread_init (gpointer vtable); ^~~~~~~~~~~~~ cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c jobqueue.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o jobqueue.test jobqueue.test.o jobqueue.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c threadref.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c threadref.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o threadref.test threadref.test.o threadref.o -lpthread -L/usr/local/lib -lglib-2.0 -lintl Making all in sequence cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c sequence.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c sequence.c sequence.c: In function 'Sequence_destroy_annotation_tree': sequence.c:97:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] g_tree_traverse(tree, Sequence_destroy_annotation_data, ^~~~~~~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:91, from sequence.h:24, from sequence.c:21: /usr/local/include/glib-2.0/glib/gtree.h:88:10: note: declared here void g_tree_traverse (GTree *tree, ^~~~~~~~~~~~~~~ cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c alphabet.c alphabet.c: In function 'Alphabet_name_get_type': alphabet.c:317:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(name, dna_string[i])) ^~ In file included from /usr/local/include/glib-2.0/glib.h:82, from alphabet.h:24, from alphabet.c:19: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ alphabet.c:320:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(name, protein_string[i])) ^~ In file included from /usr/local/include/glib-2.0/glib.h:82, from alphabet.h:24, from alphabet.c:19: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ alphabet.c:323:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(name, unknown_string[i])) ^~ In file included from /usr/local/include/glib-2.0/glib.h:82, from alphabet.h:24, from alphabet.c:19: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c translate.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c splice.c splice.c: In function 'SplicePredictor_parse_data': splice.c:146:17: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(word, "splice")) ^~ In file included from /usr/local/include/glib-2.0/glib.h:82, from splice.h:23, from splice.c:22: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ splice.c: In function 'SplicePredictor_add_5SS_data': splice.c:195:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if((!path) || (!strlen(path)) || (!g_strcasecmp(path, "primate"))) ^~ In file included from /usr/local/include/glib-2.0/glib.h:82, from splice.h:23, from splice.c:22: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ splice.c: In function 'SplicePredictor_add_3SS_data': splice.c:203:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if((!path) || (!strlen(path)) || (!g_strcasecmp(path, "primate"))) ^~ In file included from /usr/local/include/glib-2.0/glib.h:82, from splice.h:23, from splice.c:22: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o sequence.test sequence.test.o sequence.o alphabet.o translate.o splice.o ../../src/struct/matrix.o ../../src/struct/sparsecache.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c submat.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c submat.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o submat.test submat.test.o submat.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c translate.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o translate.test translate.test.o translate.o ../../src/general/argument.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c splice.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o splice.test splice.test.o splice.o ../../src/struct/matrix.o ../../src/struct/sparsecache.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c alphabet.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o alphabet.test alphabet.test.o alphabet.o ../../src/general/argument.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c codonsubmat.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c codonsubmat.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o codonsubmat.test codonsubmat.test.o codonsubmat.o ../../src/general/argument.o -lm -L/usr/local/lib -lglib-2.0 -lintl Making all in comparison cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c wordhood.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c wordhood.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o wordhood.test wordhood.test.o wordhood.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c hspset.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c hspset.c hspset.c: In function 'HSP_Display_insert': hspset.c:637:9: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] g_strdown(query_str); ^~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:82, from hspset.h:26, from hspset.c:20: /usr/local/include/glib-2.0/glib/gstrfuncs.h:208:23: note: declared here gchar* g_strdown (gchar *string); ^~~~~~~~~ hspset.c:638:9: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] g_strdown(target_str); ^~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:82, from hspset.h:26, from hspset.c:20: /usr/local/include/glib-2.0/glib/gstrfuncs.h:208:23: note: declared here gchar* g_strdown (gchar *string); ^~~~~~~~~ hspset.c:640:9: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] g_strup(query_str); ^~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:82, from hspset.h:26, from hspset.c:20: /usr/local/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here gchar* g_strup (gchar *string); ^~~~~~~ hspset.c:641:9: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] g_strup(target_str); ^~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:82, from hspset.h:26, from hspset.c:20: /usr/local/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here gchar* g_strup (gchar *string); ^~~~~~~ cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c match.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o hspset.test hspset.test.o hspset.o match.o wordhood.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/general/threadref.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c pcr.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c pcr.c pcr.c: In function 'PCR_Match_allocate': pcr.c:31:9: warning: 'g_mem_chunk_alloc' is deprecated [-Wdeprecated-declarations] pcr_match = g_chunk_new(PCR_Match, pcr->match_mem_chunk); ^~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:106, from pcr.h:23, from pcr.c:16: /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:50:17: note: declared here gpointer g_mem_chunk_alloc (GMemChunk *mem_chunk); ^~~~~~~~~~~~~~~~~ pcr.c: In function 'PCR_Probe_create': pcr.c:59:5: warning: 'g_mem_chunk_alloc' is deprecated [-Wdeprecated-declarations] register PCR_Probe *pcr_probe = g_chunk_new(PCR_Probe, ^~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:106, from pcr.h:23, from pcr.c:16: /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:50:17: note: declared here gpointer g_mem_chunk_alloc (GMemChunk *mem_chunk); ^~~~~~~~~~~~~~~~~ pcr.c: In function 'PCR_Probe_destroy': pcr.c:69:5: warning: 'g_mem_chunk_free' is deprecated [-Wdeprecated-declarations] g_mem_chunk_free(pcr->probe_mem_chunk, pcr_probe); ^~~~~~~~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:106, from pcr.h:23, from pcr.c:16: /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:54:17: note: declared here void g_mem_chunk_free (GMemChunk *mem_chunk, ^~~~~~~~~~~~~~~~ pcr.c: In function 'PCR_Sensor_create': pcr.c:155:5: warning: 'g_mem_chunk_alloc' is deprecated [-Wdeprecated-declarations] register PCR_Sensor *pcr_sensor = g_chunk_new(PCR_Sensor, ^~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:106, from pcr.h:23, from pcr.c:16: /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:50:17: note: declared here gpointer g_mem_chunk_alloc (GMemChunk *mem_chunk); ^~~~~~~~~~~~~~~~~ pcr.c: In function 'PCR_Sensor_destroy': pcr.c:174:5: warning: 'g_mem_chunk_free' is deprecated [-Wdeprecated-declarations] g_mem_chunk_free(pcr->sensor_mem_chunk, pcr_sensor); ^~~~~~~~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:106, from pcr.h:23, from pcr.c:16: /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:54:17: note: declared here void g_mem_chunk_free (GMemChunk *mem_chunk, ^~~~~~~~~~~~~~~~ pcr.c: In function 'PCR_Primer_create': pcr.c:252:5: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] g_strup(pcr_primer->forward); ^~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:82, from pcr.h:23, from pcr.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here gchar* g_strup (gchar *string); ^~~~~~~ pcr.c:253:5: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] g_strup(pcr_primer->revcomp); ^~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:82, from pcr.h:23, from pcr.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here gchar* g_strup (gchar *string); ^~~~~~~ pcr.c: In function 'PCR_create': pcr.c:357:5: warning: 'g_mem_chunk_new' is deprecated [-Wdeprecated-declarations] pcr->sensor_mem_chunk = g_mem_chunk_new("PCR_Sensor", ^~~ In file included from /usr/local/include/glib-2.0/glib.h:106, from pcr.h:23, from pcr.c:16: /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:43:17: note: declared here GMemChunk * g_mem_chunk_new (const gchar *name, ^~~~~~~~~~~~~~~ pcr.c:363:5: warning: 'g_mem_chunk_new' is deprecated [-Wdeprecated-declarations] pcr->probe_mem_chunk = g_mem_chunk_new("PCR_Probe", ^~~ In file included from /usr/local/include/glib-2.0/glib.h:106, from pcr.h:23, from pcr.c:16: /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:43:17: note: declared here GMemChunk * g_mem_chunk_new (const gchar *name, ^~~~~~~~~~~~~~~ pcr.c:366:5: warning: 'g_mem_chunk_new' is deprecated [-Wdeprecated-declarations] pcr->match_mem_chunk = g_mem_chunk_new("PCR_Match", ^~~ In file included from /usr/local/include/glib-2.0/glib.h:106, from pcr.h:23, from pcr.c:16: /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:43:17: note: declared here GMemChunk * g_mem_chunk_new (const gchar *name, ^~~~~~~~~~~~~~~ pcr.c: In function 'PCR_destroy': pcr.c:381:5: warning: 'g_mem_chunk_destroy' is deprecated [-Wdeprecated-declarations] g_mem_chunk_destroy(pcr->sensor_mem_chunk); ^~~~~~~~~~~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:106, from pcr.h:23, from pcr.c:16: /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:48:17: note: declared here void g_mem_chunk_destroy (GMemChunk *mem_chunk); ^~~~~~~~~~~~~~~~~~~ pcr.c:383:5: warning: 'g_mem_chunk_destroy' is deprecated [-Wdeprecated-declarations] g_mem_chunk_destroy(pcr->probe_mem_chunk); ^~~~~~~~~~~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:106, from pcr.h:23, from pcr.c:16: /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:48:17: note: declared here void g_mem_chunk_destroy (GMemChunk *mem_chunk); ^~~~~~~~~~~~~~~~~~~ pcr.c:384:5: warning: 'g_mem_chunk_destroy' is deprecated [-Wdeprecated-declarations] g_mem_chunk_destroy(pcr->match_mem_chunk); ^~~~~~~~~~~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:106, from pcr.h:23, from pcr.c:16: /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:48:17: note: declared here void g_mem_chunk_destroy (GMemChunk *mem_chunk); ^~~~~~~~~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o pcr.test pcr.test.o pcr.o wordhood.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/struct/fsm.o ../../src/struct/slist.o ../../src/struct/recyclebin.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c comparison.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c comparison.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o comparison.test comparison.test.o comparison.o hspset.o match.o wordhood.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/struct/recyclebin.o ../../src/struct/pqueue.o ../../src/general/threadref.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c match.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o match.test match.test.o match.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c seeder.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c seeder.c seeder.c: In function 'Seeder_decide_fsm_type': seeder.c:268:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(force_fsm, "none")) ^~ In file included from /usr/local/include/glib-2.0/glib.h:82, from seeder.h:23, from seeder.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ seeder.c:273:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(force_fsm, "normal")) ^~ In file included from /usr/local/include/glib-2.0/glib.h:82, from seeder.h:23, from seeder.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ seeder.c:275:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(force_fsm, "compact")) ^~ In file included from /usr/local/include/glib-2.0/glib.h:82, from seeder.h:23, from seeder.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o seeder.test seeder.test.o seeder.o wordhood.o hspset.o match.o comparison.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/struct/recyclebin.o ../../src/struct/fsm.o ../../src/struct/vfsm.o ../../src/struct/pqueue.o ../../src/general/threadref.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl Making all in database cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastadb.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastadb.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastadb.test fastadb.test.o fastadb.o ../../src/general/compoundfile.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastapipe.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastapipe.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastapipe.test fastapipe.test.o fastapipe.o fastadb.o ../../src/general/compoundfile.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c dataset.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c dataset.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o dataset.test dataset.test.o dataset.o fastadb.o ../../src/general/compoundfile.o ../../src/struct/bitarray.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c index.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c index.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o index.test index.test.o index.o fastadb.o dataset.o ../../src/general/compoundfile.o ../../src/general/threadref.o ../../src/struct/bitarray.o ../../src/struct/vfsm.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/struct/splaytree.o ../../src/struct/noitree.o ../../src/comparison/wordhood.o ../../src/comparison/hspset.o ../../src/comparison/match.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl Making all in c4 cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly6.1\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c region.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly6.1\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c region.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o region.test region.test.o region.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly6.1\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c c4.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly6.1\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c c4.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o c4.test c4.test.o c4.o region.o ../../src/struct/matrix.o ../../src/general/threadref.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly6.1\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c alignment.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly6.1\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c alignment.c alignment.c: In function 'AlignmentView_add_SPLICE_SITE': alignment.c:660:9: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] g_strdown(qy_seq_string); ^~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:82, from ../../src/comparison/match.h:23, from alignment.c:20: /usr/local/include/glib-2.0/glib/gstrfuncs.h:208:23: note: declared here gchar* g_strdown (gchar *string); ^~~~~~~~~ alignment.c:667:9: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] g_strdown(tg_seq_string); ^~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:82, from ../../src/comparison/match.h:23, from alignment.c:20: /usr/local/include/glib-2.0/glib/gstrfuncs.h:208:23: note: declared here gchar* g_strdown (gchar *string); ^~~~~~~~~ alignment.c:677:13: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] g_strdown(qy_seq_string); ^~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:82, from ../../src/comparison/match.h:23, from alignment.c:20: /usr/local/include/glib-2.0/glib/gstrfuncs.h:208:23: note: declared here gchar* g_strdown (gchar *string); ^~~~~~~~~ alignment.c:690:9: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] g_strdown(tg_seq_string); ^~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:82, from ../../src/comparison/match.h:23, from alignment.c:20: /usr/local/include/glib-2.0/glib/gstrfuncs.h:208:23: note: declared here gchar* g_strdown (gchar *string); ^~~~~~~~~ alignment.c: In function 'AlignmentView_add_SPLIT_CODON': alignment.c:987:5: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] g_strup(qy_codon); ^~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:82, from ../../src/comparison/match.h:23, from alignment.c:20: /usr/local/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here gchar* g_strup (gchar *string); ^~~~~~~ alignment.c:988:5: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] g_strup(tg_codon); ^~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:82, from ../../src/comparison/match.h:23, from alignment.c:20: /usr/local/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here gchar* g_strup (gchar *string); ^~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o alignment.test alignment.test.o alignment.o c4.o region.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/general/threadref.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly6.1\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c codegen.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly6.1\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c codegen.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o codegen.test codegen.test.o codegen.o ../../src/general/argument.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly6.1\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c optimal.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly6.1\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c optimal.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly6.1\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c layout.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly6.1\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c viterbi.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly6.1\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c subopt.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly6.1\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c cgutil.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o optimal.test optimal.test.o optimal.o c4.o alignment.o codegen.o region.o layout.o viterbi.o subopt.o cgutil.o ../../src/struct/slist.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/general/threadref.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly6.1\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c layout.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o layout.test layout.test.o layout.o ../../src/struct/matrix.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly6.1\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c viterbi.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o viterbi.test viterbi.test.o viterbi.o c4.o region.o alignment.o codegen.o layout.o subopt.o cgutil.o ../../src/struct/slist.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/general/threadref.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly6.1\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c opair.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly6.1\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c opair.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o opair.test opair.test.o opair.o optimal.o c4.o alignment.o codegen.o region.o layout.o viterbi.o subopt.o cgutil.o ../../src/struct/slist.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/general/threadref.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly6.1\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c subopt.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o subopt.test subopt.test.o subopt.o region.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly6.1\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c cgutil.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o cgutil.test cgutil.test.o cgutil.o codegen.o c4.o region.o ../../src/general/argument.o ../../src/struct/matrix.o ../../src/general/threadref.o -L/usr/local/lib -lglib-2.0 -lintl Making all in bsdp cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly6.1\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c heuristic.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly6.1\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c heuristic.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o heuristic.test heuristic.test.o heuristic.o ../../src/struct/slist.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/c4/c4.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/codegen.o ../../src/c4/region.o ../../src/c4/layout.o ../../src/c4/viterbi.o ../../src/c4/subopt.o ../../src/c4/cgutil.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly6.1\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c bsdp.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly6.1\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c bsdp.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o bsdp.test bsdp.test.o bsdp.o ../../src/general/argument.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly6.1\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c hpair.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly6.1\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c hpair.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly6.1\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c sar.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o hpair.test hpair.test.o hpair.o heuristic.o bsdp.o sar.o ../../src/struct/slist.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/comparison/hspset.o ../../src/comparison/wordhood.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/c4/c4.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/codegen.o ../../src/c4/region.o ../../src/c4/layout.o ../../src/c4/viterbi.o ../../src/c4/subopt.o ../../src/c4/cgutil.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly6.1\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c sar.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o sar.test sar.test.o sar.o heuristic.o ../../src/struct/slist.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/c4/c4.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/codegen.o ../../src/c4/region.o ../../src/c4/layout.o ../../src/c4/viterbi.o ../../src/c4/subopt.o ../../src/c4/cgutil.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl Making all in sdp cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly6.1\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c sdp.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly6.1\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c sdp.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly6.1\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c boundary.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly6.1\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c scheduler.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly6.1\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c lookahead.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly6.1\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c straceback.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o sdp.test sdp.test.o sdp.o boundary.o scheduler.o lookahead.o straceback.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/comparison/hspset.o ../../src/comparison/comparison.o ../../src/comparison/wordhood.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/c4/c4.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/codegen.o ../../src/c4/region.o ../../src/c4/layout.o ../../src/c4/viterbi.o ../../src/c4/subopt.o ../../src/c4/cgutil.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly6.1\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c lookahead.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o lookahead.test lookahead.test.o lookahead.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly6.1\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c boundary.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o boundary.test boundary.test.o boundary.o ../../src/general/argument.o ../../src/c4/region.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly6.1\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c scheduler.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o scheduler.test scheduler.test.o scheduler.o lookahead.o boundary.o straceback.o ../../src/struct/recyclebin.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/c4/c4.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/codegen.o ../../src/c4/region.o ../../src/c4/layout.o ../../src/c4/viterbi.o ../../src/c4/subopt.o ../../src/c4/cgutil.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly6.1\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c straceback.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o straceback.test straceback.test.o straceback.o ../../src/struct/recyclebin.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/c4/c4.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/codegen.o ../../src/c4/region.o ../../src/c4/layout.o ../../src/c4/viterbi.o ../../src/c4/subopt.o ../../src/c4/cgutil.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl Making all in model cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c edit_distance.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c edit_distance.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o edit_distance.test edit_distance.test.o edit_distance.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c affine.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c affine.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c ungapped.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o affine.test affine.test.o affine.o ungapped.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c protein2dna.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c protein2dna.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c frameshift.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o protein2dna.test protein2dna.test.o protein2dna.o affine.o ungapped.o frameshift.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c ner.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c ner.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o ner.test ner.test.o ner.o affine.o ungapped.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c est2genome.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c est2genome.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c intron.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o est2genome.test est2genome.test.o est2genome.o affine.o ungapped.o intron.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c ungapped.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o ungapped.test ungapped.test.o ungapped.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c intron.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o intron.test intron.test.o intron.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c protein2genome.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c protein2genome.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c phase.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o protein2genome.test protein2genome.test.o protein2genome.o protein2dna.o ungapped.o intron.o affine.o frameshift.o phase.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c coding2coding.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c coding2coding.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o coding2coding.test coding2coding.test.o coding2coding.o affine.o ungapped.o frameshift.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c frameshift.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o frameshift.test frameshift.test.o frameshift.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c coding2genome.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c coding2genome.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o coding2genome.test coding2genome.test.o coding2genome.o coding2coding.o affine.o ungapped.o frameshift.o intron.o phase.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c cdna2genome.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c cdna2genome.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o cdna2genome.test cdna2genome.test.o cdna2genome.o affine.o ungapped.o frameshift.o intron.o phase.o coding2coding.o coding2genome.o est2genome.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c genome2genome.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c genome2genome.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o genome2genome.test genome2genome.test.o genome2genome.o coding2coding.o affine.o ungapped.o frameshift.o intron.o phase.o coding2genome.o cdna2genome.o est2genome.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c phase.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o phase.test phase.test.o phase.o intron.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c modeltype.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c modeltype.c modeltype.c: In function 'Model_Type_from_string': modeltype.c:121:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(name[i], str)) ^~ In file included from /usr/local/include/glib-2.0/glib.h:82, from ../../src/c4/c4.h:23, from modeltype.h:23, from modeltype.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ modeltype.c:124:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(short_name[i], str)) ^~ In file included from /usr/local/include/glib-2.0/glib.h:82, from ../../src/c4/c4.h:23, from modeltype.h:23, from modeltype.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o modeltype.test modeltype.test.o modeltype.o ungapped.o affine.o est2genome.o ner.o protein2dna.o protein2genome.o coding2coding.o coding2genome.o genome2genome.o cdna2genome.o frameshift.o phase.o intron.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c bootstrapper.c bootstrapper.c: In function 'Argument_main': bootstrapper.c:421:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if((!models) || (!g_strcasecmp(models, "all"))) ^~ In file included from /usr/local/include/glib-2.0/glib.h:82, from ../../src/c4/c4.h:23, from ungapped.h:23, from bootstrapper.c:20: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o bootstrapper bootstrapper.o modeltype.o ungapped.o affine.o est2genome.o ner.o protein2dna.o protein2genome.o coding2coding.o coding2genome.o genome2genome.o cdna2genome.o frameshift.o intron.o phase.o ../../src/struct/pqueue.o ../../src/comparison/comparison.o ../../src/comparison/hspset.o ../../src/comparison/wordhood.o ../../src/bsdp/heuristic.o ../../src/sdp/sdp.o ../../src/sdp/scheduler.o ../../src/sdp/straceback.o ../../src/sdp/lookahead.o ../../src/sdp/boundary.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl Making all in hub cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/general -DHOSTTYPE="\"x86_64-portbld-dragonfly6.1\"" -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c gam.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/general -DHOSTTYPE="\"x86_64-portbld-dragonfly6.1\"" -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c gam.c gam.c: In function 'GAM_Refinement_from_string': gam.c:68:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(name[i], str)) ^~ In file included from /usr/local/include/glib-2.0/glib.h:82, from gam.h:23, from gam.c:21: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ gam.c: In function 'GAM_bestn_tree_destroy': gam.c:526:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] g_tree_traverse(bestn_tree, GAM_tree_collect_values, ^~~~~~~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:91, from gam.h:23, from gam.c:21: /usr/local/include/glib-2.0/glib/gtree.h:88:10: note: declared here void g_tree_traverse (GTree *tree, ^~~~~~~~~~~~~~~ gam.c: In function 'GAM_percent_threshold_tree_destroy': gam.c:539:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] g_tree_traverse(percent_threshold_tree, GAM_tree_collect_values, ^~~~~~~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:91, from gam.h:23, from gam.c:21: /usr/local/include/glib-2.0/glib/gtree.h:88:10: note: declared here void g_tree_traverse (GTree *tree, ^~~~~~~~~~~~~~~ gam.c: In function 'GAM_report': gam.c:589:9: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] g_tree_traverse(gam->bestn_tree, GAM_bestn_tree_report_traverse, ^~~~~~~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:91, from gam.h:23, from gam.c:21: /usr/local/include/glib-2.0/glib/gtree.h:88:10: note: declared here void g_tree_traverse (GTree *tree, ^~~~~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o gam.test gam.test.o gam.o ../../src/comparison/hspset.o ../../src/comparison/comparison.o ../../src/comparison/wordhood.o ../../src/struct/sparsecache.o ../../src/general/compoundfile.o ../../src/general/threadref.o ../../src/c4/c4.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/opair.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/region.o ../../src/c4/subopt.o ../../src/bsdp/bsdp.o ../../src/bsdp/sar.o ../../src/bsdp/heuristic.o ../../src/bsdp/hpair.o ../../src/sdp/boundary.o ../../src/sdp/sdp.o ../../src/sdp/scheduler.o ../../src/sdp/straceback.o ../../src/sdp/lookahead.o ../../src/struct/matrix.o ../../src/struct/slist.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/translate.o ../../src/sequence/splice.o ../../src/model/affine.o ../../src/model/est2genome.o ../../src/model/ner.o ../../src/model/protein2dna.o ../../src/model/protein2genome.o ../../src/model/coding2coding.o ../../src/model/coding2genome.o ../../src/model/cdna2genome.o ../../src/model/genome2genome.o ../../src/model/ungapped.o ../../src/model/intron.o ../../src/model/frameshift.o ../../src/model/phase.o ../../src/model/modeltype.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/jobqueue.o ../../src/comparison/match.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/general -DHOSTTYPE="\"x86_64-portbld-dragonfly6.1\"" -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c analysis.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/general -DHOSTTYPE="\"x86_64-portbld-dragonfly6.1\"" -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c analysis.c analysis.c: In function 'Analysis_decide_scan_query': analysis.c:329:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(force_scan, "none")){ ^~ In file included from /usr/local/include/glib-2.0/glib.h:82, from analysis.h:23, from analysis.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ analysis.c:336:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] } else if((!g_strcasecmp(force_scan, "query")) ^ In file included from /usr/local/include/glib-2.0/glib.h:82, from analysis.h:23, from analysis.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ analysis.c:337:12: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] || (!g_strcasecmp(force_scan, "q"))){ ^~ In file included from /usr/local/include/glib-2.0/glib.h:82, from analysis.h:23, from analysis.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ analysis.c:339:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] } else if((!g_strcasecmp(force_scan, "target")) ^ In file included from /usr/local/include/glib-2.0/glib.h:82, from analysis.h:23, from analysis.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ analysis.c:340:12: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] || (!g_strcasecmp(force_scan, "t"))){ ^~ In file included from /usr/local/include/glib-2.0/glib.h:82, from analysis.h:23, from analysis.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/general -DHOSTTYPE="\"x86_64-portbld-dragonfly6.1\"" -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c bsam.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o analysis.test analysis.test.o analysis.o gam.o bsam.o ../../src/comparison/hspset.o ../../src/comparison/wordhood.o ../../src/comparison/seeder.o ../../src/comparison/comparison.o ../../src/database/fastapipe.o ../../src/database/fastadb.o ../../src/struct/dejavu.o ../../src/struct/fsm.o ../../src/struct/vfsm.o ../../src/struct/sparsecache.o ../../src/general/compoundfile.o ../../src/general/socket.o ../../src/general/threadref.o ../../src/c4/c4.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/opair.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/region.o ../../src/c4/subopt.o ../../src/bsdp/bsdp.o ../../src/bsdp/sar.o ../../src/bsdp/heuristic.o ../../src/bsdp/hpair.o ../../src/sdp/boundary.o ../../src/sdp/sdp.o ../../src/sdp/scheduler.o ../../src/sdp/straceback.o ../../src/sdp/lookahead.o ../../src/struct/matrix.o ../../src/struct/slist.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/translate.o ../../src/sequence/splice.o ../../src/model/affine.o ../../src/model/est2genome.o ../../src/model/ner.o ../../src/model/protein2dna.o ../../src/model/protein2genome.o ../../src/model/coding2coding.o ../../src/model/coding2genome.o ../../src/model/cdna2genome.o ../../src/model/genome2genome.o ../../src/model/ungapped.o ../../src/model/intron.o ../../src/model/frameshift.o ../../src/model/phase.o ../../src/model/modeltype.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/jobqueue.o ../../src/comparison/match.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/general -DHOSTTYPE="\"x86_64-portbld-dragonfly6.1\"" -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c bsam.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o bsam.test bsam.test.o bsam.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o ../../src/comparison/hspset.o ../../src/comparison/comparison.o ../../src/comparison/match.o ../../src/comparison/wordhood.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/translate.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/sequence/splice.o ../../src/struct/dejavu.o ../../src/struct/pqueue.o ../../src/struct/sparsecache.o ../../src/struct/recyclebin.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl Making all in program cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/hub -I../../src/general -DHOSTTYPE="\"x86_64-portbld-dragonfly6.1\"" -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c exonerate.c ../../src/model/bootstrapper --compiled no ** Message: 20:20:25.506: Starting building bootstrapping components ** Message: 20:20:25.506: Processing model [u] ** Message: 20:20:25.507: Bootstrapper processing model [ungapped:dna2dna] ** Message: 20:20:25.507: Process optimal [optimal:ungapped:dna2dna] ** (process:288505): WARNING **: 20:20:25.507: Creating codegen directory [/construction/biology/exonerate/exonerate-2.4.0/codegen] ** (process:288505): WARNING **: 20:20:25.507: Creating codegen directory [/construction/biology/exonerate/exonerate-2.4.0/codegen] ** (process:288505): WARNING **: 20:20:25.507: Creating codegen directory [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1] ** (process:288505): WARNING **: 20:20:25.507: Creating codegen directory [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1] ** Message: 20:20:25.508: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_dna2dna_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_dna2dna_32_find_32_score.c ** Message: 20:20:25.837: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_dna2dna_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_dna2dna_32_find_32_path.c ** Message: 20:20:26.238: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_dna2dna_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_dna2dna_32_find_32_region.c ** Message: 20:20:26.611: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.c ** Message: 20:20:27.407: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 20:20:28.292: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_dna2dna_32_find_32_score.o] ** Message: 20:20:28.292: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_dna2dna_32_find_32_score.o] to archive ar -cSq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_dna2dna_32_find_32_score.o ** Message: 20:20:28.301: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_score] ** Message: 20:20:28.301: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_dna2dna_32_find_32_path.o] ** Message: 20:20:28.301: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_dna2dna_32_find_32_path.o ** Message: 20:20:28.307: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_path] ** Message: 20:20:28.307: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_dna2dna_32_find_32_region.o] ** Message: 20:20:28.307: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_dna2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_dna2dna_32_find_32_region.o ** Message: 20:20:28.313: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_region] ** Message: 20:20:28.313: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.o] ** Message: 20:20:28.313: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.o ** Message: 20:20:28.319: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint] ** Message: 20:20:28.319: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 20:20:28.320: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 20:20:28.326: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation] ** Message: 20:20:28.327: Bootstrapper processing model [ungapped:protein2protein] ** Message: 20:20:28.327: Process optimal [optimal:ungapped:protein2protein] ** Message: 20:20:28.327: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_protein2protein_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_protein2protein_32_find_32_score.c ** Message: 20:20:28.595: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_protein2protein_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_protein2protein_32_find_32_path.c ** Message: 20:20:28.923: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_protein2protein_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_protein2protein_32_find_32_region.c ** Message: 20:20:29.456: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.c ** Message: 20:20:30.129: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.c ** Message: 20:20:31.013: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_protein2protein_32_find_32_score.o] ** Message: 20:20:31.014: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_protein2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_protein2protein_32_find_32_score.o ** Message: 20:20:31.020: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_score] ** Message: 20:20:31.021: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_protein2protein_32_find_32_path.o] ** Message: 20:20:31.021: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_protein2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_protein2protein_32_find_32_path.o ** Message: 20:20:31.026: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_path] ** Message: 20:20:31.026: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_protein2protein_32_find_32_region.o] ** Message: 20:20:31.026: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_protein2protein_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_protein2protein_32_find_32_region.o ** Message: 20:20:31.032: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_region] ** Message: 20:20:31.032: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.o] ** Message: 20:20:31.032: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.o ** Message: 20:20:31.037: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint] ** Message: 20:20:31.038: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.o] ** Message: 20:20:31.038: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.o ** Message: 20:20:31.043: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation] ** Message: 20:20:31.044: Bootstrapper processing model [ungapped:dna2protein] ** Message: 20:20:31.044: Process optimal [optimal:ungapped:dna2protein] ** Message: 20:20:31.044: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_dna2protein_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_dna2protein_32_find_32_score.c ** Message: 20:20:31.491: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_dna2protein_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_dna2protein_32_find_32_path.c ** Message: 20:20:32.098: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_dna2protein_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_dna2protein_32_find_32_region.c ** Message: 20:20:32.731: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.c ** Message: 20:20:33.514: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.c ** Message: 20:20:34.832: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_dna2protein_32_find_32_score.o] ** Message: 20:20:34.832: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_dna2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_dna2protein_32_find_32_score.o ** Message: 20:20:34.839: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_score] ** Message: 20:20:34.839: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_dna2protein_32_find_32_path.o] ** Message: 20:20:34.839: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_dna2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_dna2protein_32_find_32_path.o ** Message: 20:20:34.845: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_path] ** Message: 20:20:34.845: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_dna2protein_32_find_32_region.o] ** Message: 20:20:34.845: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_dna2protein_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_dna2protein_32_find_32_region.o ** Message: 20:20:34.852: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_region] ** Message: 20:20:34.852: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.o] ** Message: 20:20:34.852: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.o ** Message: 20:20:34.858: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint] ** Message: 20:20:34.858: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.o] ** Message: 20:20:34.858: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.o ** Message: 20:20:34.864: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation] ** Message: 20:20:34.865: Bootstrapper processing model [ungapped:protein2dna] ** Message: 20:20:34.865: Process optimal [optimal:ungapped:protein2dna] ** Message: 20:20:34.865: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_protein2dna_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_protein2dna_32_find_32_score.c ** Message: 20:20:35.242: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_protein2dna_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_protein2dna_32_find_32_path.c ** Message: 20:20:35.965: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_protein2dna_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_protein2dna_32_find_32_region.c ** Message: 20:20:36.606: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.c ** Message: 20:20:37.835: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.c ** Message: 20:20:38.694: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_protein2dna_32_find_32_score.o] ** Message: 20:20:38.695: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_protein2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_protein2dna_32_find_32_score.o ** Message: 20:20:38.702: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_score] ** Message: 20:20:38.702: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_protein2dna_32_find_32_path.o] ** Message: 20:20:38.702: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_protein2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_protein2dna_32_find_32_path.o ** Message: 20:20:38.709: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_path] ** Message: 20:20:38.709: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_protein2dna_32_find_32_region.o] ** Message: 20:20:38.709: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_protein2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_protein2dna_32_find_32_region.o ** Message: 20:20:38.716: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_region] ** Message: 20:20:38.716: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.o] ** Message: 20:20:38.716: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.o ** Message: 20:20:38.722: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint] ** Message: 20:20:38.723: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.o] ** Message: 20:20:38.723: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.o ** Message: 20:20:38.729: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation] ** Message: 20:20:38.729: Processing model [u:t] ** Message: 20:20:38.730: Bootstrapper processing model [ungapped:codon] ** Message: 20:20:38.730: Process optimal [optimal:ungapped:codon] ** Message: 20:20:38.730: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_codon_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_codon_32_find_32_score.c ** Message: 20:20:39.234: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_codon_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_codon_32_find_32_path.c ** Message: 20:20:39.945: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_codon_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_codon_32_find_32_region.c ** Message: 20:20:40.913: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_codon_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_codon_32_find_32_checkpoint.c ** Message: 20:20:42.439: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.c ** Message: 20:20:44.517: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_codon_32_find_32_score.o] ** Message: 20:20:44.517: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_codon_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_codon_32_find_32_score.o ** Message: 20:20:44.524: Adding function [optimal_58_ungapped_58_codon_32_find_32_score] ** Message: 20:20:44.524: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_codon_32_find_32_path.o] ** Message: 20:20:44.524: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_codon_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_codon_32_find_32_path.o ** Message: 20:20:44.541: Adding function [optimal_58_ungapped_58_codon_32_find_32_path] ** Message: 20:20:44.541: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_codon_32_find_32_region.o] ** Message: 20:20:44.541: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_codon_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_codon_32_find_32_region.o ** Message: 20:20:44.548: Adding function [optimal_58_ungapped_58_codon_32_find_32_region] ** Message: 20:20:44.548: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_codon_32_find_32_checkpoint.o] ** Message: 20:20:44.548: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_codon_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_codon_32_find_32_checkpoint.o ** Message: 20:20:44.554: Adding function [optimal_58_ungapped_58_codon_32_find_32_checkpoint] ** Message: 20:20:44.554: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.o] ** Message: 20:20:44.554: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.o ** Message: 20:20:44.561: Adding function [optimal_58_ungapped_58_codon_32_find_32_path_32_continuation] ** Message: 20:20:44.561: Processing model [a:g] ** Message: 20:20:44.561: Bootstrapper processing model [affine:global:dna2dna] ** Message: 20:20:44.561: Process optimal [optimal:affine:global:dna2dna] ** Message: 20:20:44.563: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.c ** Message: 20:20:45.339: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.c ** Message: 20:20:46.791: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.c ** Message: 20:20:48.125: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 20:20:49.798: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.o] ** Message: 20:20:49.799: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.o ** Message: 20:20:49.805: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_score] ** Message: 20:20:49.805: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.o] ** Message: 20:20:49.806: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.o ** Message: 20:20:49.813: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_path] ** Message: 20:20:49.813: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.o] ** Message: 20:20:49.813: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.o ** Message: 20:20:49.820: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint] ** Message: 20:20:49.820: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 20:20:49.820: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 20:20:49.827: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation] ** Message: 20:20:49.828: Bootstrapper processing model [affine:global:protein2protein] ** Message: 20:20:49.828: Process optimal [optimal:affine:global:protein2protein] ** Message: 20:20:49.829: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.c ** Message: 20:20:50.998: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.c ** Message: 20:20:52.088: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.c ** Message: 20:20:53.738: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.c ** Message: 20:20:55.090: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.o] ** Message: 20:20:55.091: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.o ** Message: 20:20:55.098: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_score] ** Message: 20:20:55.098: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.o] ** Message: 20:20:55.098: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.o ** Message: 20:20:55.105: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_path] ** Message: 20:20:55.105: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.o] ** Message: 20:20:55.105: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.o ** Message: 20:20:55.112: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint] ** Message: 20:20:55.112: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.o] ** Message: 20:20:55.112: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.o ** Message: 20:20:55.119: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation] ** Message: 20:20:55.122: Processing model [a:b] ** Message: 20:20:55.122: Bootstrapper processing model [affine:bestfit:dna2dna] ** Message: 20:20:55.122: Process optimal [optimal:affine:bestfit:dna2dna] ** Message: 20:20:55.124: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.c ** Message: 20:20:56.367: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.c ** Message: 20:20:58.187: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.c ** Message: 20:21:00.270: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.c ** Message: 20:21:02.050: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 20:21:04.309: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.o] ** Message: 20:21:04.309: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.o ** Message: 20:21:04.318: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score] ** Message: 20:21:04.318: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.o] ** Message: 20:21:04.318: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.o ** Message: 20:21:04.325: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path] ** Message: 20:21:04.325: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.o] ** Message: 20:21:04.326: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.o ** Message: 20:21:04.334: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region] ** Message: 20:21:04.334: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.o] ** Message: 20:21:04.334: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.o ** Message: 20:21:04.341: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint] ** Message: 20:21:04.341: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 20:21:04.342: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 20:21:04.350: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation] ** Message: 20:21:04.351: Bootstrapper processing model [affine:bestfit:protein2protein] ** Message: 20:21:04.351: Process optimal [optimal:affine:bestfit:protein2protein] ** Message: 20:21:04.352: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.c ** Message: 20:21:05.798: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.c ** Message: 20:21:09.852: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.c ** Message: 20:21:12.671: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.c ** Message: 20:21:13.862: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.c ** Message: 20:21:16.729: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.o] ** Message: 20:21:16.729: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.o ** Message: 20:21:16.736: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score] ** Message: 20:21:16.736: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.o] ** Message: 20:21:16.736: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.o ** Message: 20:21:16.744: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path] ** Message: 20:21:16.745: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.o] ** Message: 20:21:16.746: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.o ** Message: 20:21:16.753: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region] ** Message: 20:21:16.753: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.o] ** Message: 20:21:16.755: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.o ** Message: 20:21:16.763: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint] ** Message: 20:21:16.763: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.o] ** Message: 20:21:16.763: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.o ** Message: 20:21:16.771: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation] ** Message: 20:21:16.771: Processing model [a:l] ** Message: 20:21:16.772: Bootstrapper processing model [affine:local:dna2dna] ** Message: 20:21:16.772: Process optimal [optimal:affine:local:dna2dna] ** Message: 20:21:16.773: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.c ** Message: 20:21:17.265: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.c ** Message: 20:21:18.646: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.c ** Message: 20:21:19.469: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.c ** Message: 20:21:21.510: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 20:21:22.956: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.o] ** Message: 20:21:22.956: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.o ** Message: 20:21:22.967: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_score] ** Message: 20:21:22.967: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.o] ** Message: 20:21:22.967: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.o ** Message: 20:21:22.975: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_path] ** Message: 20:21:22.976: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.o] ** Message: 20:21:22.976: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.o ** Message: 20:21:22.984: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_region] ** Message: 20:21:22.984: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o] ** Message: 20:21:22.985: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o ** Message: 20:21:22.993: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint] ** Message: 20:21:22.993: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 20:21:22.995: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 20:21:23.005: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation] ** Message: 20:21:23.008: Process optimal [Terminal [Segment("START"->"match"):[affine:local:dna2dna]]] ** Message: 20:21:23.010: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:21:24.739: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:21:27.634: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:21:27.634: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:21:27.643: 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: 20:21:27.643: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:21:27.644: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:21:27.654: 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: 20:21:27.654: Process optimal [Terminal [Segment("match"->"END"):[affine:local:dna2dna]]] ** Message: 20:21:27.656: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:21:28.455: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:21:29.909: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:21:29.909: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:21:29.917: 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: 20:21:29.917: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:21:29.917: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:21:29.936: 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: 20:21:29.936: Process optimal [HeuristicJoin:[Segment("match"->"match"):[affine:local:dna2dna]]] ** Message: 20:21:29.939: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:21:35.812: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:21:43.892: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:21:43.892: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:21:43.901: 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: 20:21:43.901: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:21:43.901: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:21:43.909: 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: 20:21:43.910: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.c ** Message: 20:21:44.464: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.c ** Message: 20:21:44.971: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.o] ** Message: 20:21:44.971: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.o ** Message: 20:21:44.980: Adding function [Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded] ** Message: 20:21:44.980: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.o] ** Message: 20:21:44.980: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.o ** Message: 20:21:44.988: Adding function [Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded] ** Message: 20:21:44.989: Bootstrapper processing model [affine:local:protein2protein] ** Message: 20:21:44.989: Process optimal [optimal:affine:local:protein2protein] ** Message: 20:21:44.990: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.c ** Message: 20:21:45.780: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.c ** Message: 20:21:47.252: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.c ** Message: 20:21:48.078: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.c ** Message: 20:21:50.142: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.c ** Message: 20:21:52.489: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.o] ** Message: 20:21:52.490: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.o ** Message: 20:21:52.498: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_score] ** Message: 20:21:52.498: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.o] ** Message: 20:21:52.498: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.o ** Message: 20:21:52.506: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_path] ** Message: 20:21:52.507: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.o] ** Message: 20:21:52.507: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.o ** Message: 20:21:52.516: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_region] ** Message: 20:21:52.516: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o] ** Message: 20:21:52.516: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o ** Message: 20:21:52.526: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint] ** Message: 20:21:52.526: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o] ** Message: 20:21:52.526: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o ** Message: 20:21:52.535: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation] ** Message: 20:21:52.538: Process optimal [Terminal [Segment("START"->"match"):[affine:local:protein2protein]]] ** Message: 20:21:52.540: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:21:53.864: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:21:56.367: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:21:56.368: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:21:56.376: 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: 20:21:56.376: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:21:56.376: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:21:56.386: 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: 20:21:56.386: Process optimal [Terminal [Segment("match"->"END"):[affine:local:protein2protein]]] ** Message: 20:21:56.387: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:21:57.848: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:21:58.807: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:21:58.808: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:21:58.817: 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: 20:21:58.817: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:21:58.817: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:21:58.826: 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: 20:21:58.826: Process optimal [HeuristicJoin:[Segment("match"->"match"):[affine:local:protein2protein]]] ** Message: 20:21:58.829: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:22:00.659: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:22:04.184: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:22:04.189: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:22:04.198: 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: 20:22:04.198: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:22:04.198: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:22:04.207: 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: 20:22:04.208: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.c ** Message: 20:22:04.539: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.c ** Message: 20:22:04.980: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.o] ** Message: 20:22:04.980: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.o ** Message: 20:22:04.989: Adding function [Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded] ** Message: 20:22:04.990: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.o] ** Message: 20:22:04.990: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.o ** Message: 20:22:04.999: Adding function [Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded] ** Message: 20:22:04.999: Processing model [a:o] ** Message: 20:22:05.000: Bootstrapper processing model [affine:overlap:dna2dna] ** Message: 20:22:05.000: Process optimal [optimal:affine:overlap:dna2dna] ** Message: 20:22:05.002: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.c ** Message: 20:22:06.194: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.c ** Message: 20:22:07.982: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.c ** Message: 20:22:10.454: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.c ** Message: 20:22:11.902: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 20:22:13.312: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.o] ** Message: 20:22:13.314: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.o ** Message: 20:22:13.324: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score] ** Message: 20:22:13.325: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.o] ** Message: 20:22:13.325: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.o ** Message: 20:22:13.335: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path] ** Message: 20:22:13.335: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.o] ** Message: 20:22:13.335: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.o ** Message: 20:22:13.345: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region] ** Message: 20:22:13.346: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.o] ** Message: 20:22:13.346: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.o ** Message: 20:22:13.355: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint] ** Message: 20:22:13.356: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 20:22:13.356: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 20:22:13.365: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation] ** Message: 20:22:13.366: Processing model [e2g] ** Message: 20:22:13.367: Bootstrapper processing model [est2genome] ** Message: 20:22:13.367: Process optimal [optimal:est2genome] ** Message: 20:22:13.369: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_est2genome_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_est2genome_32_find_32_score.c ** Message: 20:22:15.938: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_est2genome_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_est2genome_32_find_32_path.c ** Message: 20:22:19.788: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_est2genome_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_est2genome_32_find_32_region.c ** Message: 20:22:22.025: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_est2genome_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_est2genome_32_find_32_checkpoint.c ** Message: 20:22:29.608: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_est2genome_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_est2genome_32_find_32_path_32_continuation.c ** Message: 20:22:42.963: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_est2genome_32_find_32_score.o] ** Message: 20:22:42.963: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_est2genome_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_est2genome_32_find_32_score.o ** Message: 20:22:42.973: Adding function [optimal_58_est2genome_32_find_32_score] ** Message: 20:22:42.973: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_est2genome_32_find_32_path.o] ** Message: 20:22:42.973: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_est2genome_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_est2genome_32_find_32_path.o ** Message: 20:22:42.982: Adding function [optimal_58_est2genome_32_find_32_path] ** Message: 20:22:42.982: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_est2genome_32_find_32_region.o] ** Message: 20:22:42.982: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_est2genome_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_est2genome_32_find_32_region.o ** Message: 20:22:42.992: Adding function [optimal_58_est2genome_32_find_32_region] ** Message: 20:22:42.992: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_est2genome_32_find_32_checkpoint.o] ** Message: 20:22:42.992: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_est2genome_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_est2genome_32_find_32_checkpoint.o ** Message: 20:22:43.002: Adding function [optimal_58_est2genome_32_find_32_checkpoint] ** Message: 20:22:43.002: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_est2genome_32_find_32_path_32_continuation.o] ** Message: 20:22:43.003: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_est2genome_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_est2genome_32_find_32_path_32_continuation.o ** Message: 20:22:43.012: Adding function [optimal_58_est2genome_32_find_32_path_32_continuation] ** Message: 20:22:43.024: Process optimal [Terminal [Segment("START"->"match reverse"):[est2genome]]] ** Message: 20:22:43.027: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:22:48.957: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:22:57.409: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:22:57.409: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:22:57.420: 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: 20:22:57.421: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:22:57.421: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:22:57.431: 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: 20:22:57.431: Process optimal [Terminal [Segment("match reverse"->"END"):[est2genome]]] ** Message: 20:22:57.434: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:23:00.319: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:23:04.030: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:23:04.030: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:23:04.041: 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: 20:23:04.041: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:23:04.041: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:23:04.052: 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: 20:23:04.053: Process optimal [Terminal [Segment("START"->"match forward"):[est2genome]]] ** Message: 20:23:04.056: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:23:09.066: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:23:16.862: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:23:16.862: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:23:16.872: 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: 20:23:16.872: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:23:16.872: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:23:16.883: 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: 20:23:16.883: Process optimal [Terminal [Segment("match forward"->"END"):[est2genome]]] ** Message: 20:23:16.885: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:23:18.682: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:23:22.047: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:23:22.048: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:23:22.069: 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: 20:23:22.069: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:23:22.069: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:23:22.079: 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: 20:23:22.080: Process optimal [HeuristicJoin:[Segment("match reverse"->"match reverse"):[est2genome]]] ** Message: 20:23:22.085: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:23:31.838: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:23:49.359: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:23:49.359: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:23:49.370: 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: 20:23:49.370: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:23:49.370: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:23:49.401: 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: 20:23:49.401: Process optimal [Src span [Segment("match reverse"->"intron reverse"):[est2genome]]] ** Message: 20:23:49.403: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:23:51.272: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:23:55.732: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:23:55.732: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:23:55.743: 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: 20:23:55.743: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:23:55.743: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:23:55.754: 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: 20:23:55.755: Process optimal [Src span traceback [Segment("match reverse"->"intron reverse"):[est2genome]]] ** Message: 20:23:55.760: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:24:08.221: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:24:08.221: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:24:08.233: 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: 20:24:08.233: Process optimal [Dst span [Segment("intron reverse"->"match reverse"):[est2genome]]] ** Message: 20:24:08.236: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:24:13.419: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:24:20.019: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:24:20.019: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:24:20.030: 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: 20:24:20.031: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:24:20.031: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:24:20.042: 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: 20:24:20.042: Process optimal [HeuristicJoin:[Segment("match forward"->"match forward"):[est2genome]]] ** Message: 20:24:20.047: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:24:27.278: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:24:42.795: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:24:42.795: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:24:42.808: 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: 20:24:42.808: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:24:42.808: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:24:42.821: 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: 20:24:42.821: Process optimal [Src span [Segment("match forward"->"intron forward"):[est2genome]]] ** Message: 20:24:42.823: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:24:44.750: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:24:47.872: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:24:47.872: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:24:47.886: 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: 20:24:47.886: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:24:47.886: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:24:47.910: 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: 20:24:47.911: Process optimal [Src span traceback [Segment("match forward"->"intron forward"):[est2genome]]] ** Message: 20:24:47.916: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:24:57.143: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:24:57.143: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:24:57.156: 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: 20:24:57.157: Process optimal [Dst span [Segment("intron forward"->"match forward"):[est2genome]]] ** Message: 20:24:57.160: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:25:01.190: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:25:15.742: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:25:15.742: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:25:15.756: 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: 20:25:15.756: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:25:15.757: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:25:15.769: 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: 20:25:15.771: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.c ** Message: 20:25:17.208: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.c ** Message: 20:25:19.038: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.o] ** Message: 20:25:19.038: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.o ** Message: 20:25:19.051: Adding function [Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary] ** Message: 20:25:19.051: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.o] ** Message: 20:25:19.051: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.o ** Message: 20:25:19.065: Adding function [Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary] ** Message: 20:25:19.065: Processing model [ner] ** Message: 20:25:19.066: Bootstrapper processing model [NER:affine:local:dna2dna] ** Message: 20:25:19.066: Process optimal [optimal:NER:affine:local:dna2dna] ** Message: 20:25:19.066: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.c ** Message: 20:25:19.580: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.c ** Message: 20:25:21.135: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.c ** Message: 20:25:21.676: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.c ** Message: 20:25:24.610: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 20:25:28.989: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.o] ** Message: 20:25:28.989: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.o ** Message: 20:25:29.002: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score] ** Message: 20:25:29.003: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.o] ** Message: 20:25:29.003: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.o ** Message: 20:25:29.015: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path] ** Message: 20:25:29.015: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.o] ** Message: 20:25:29.015: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.o ** Message: 20:25:29.028: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region] ** Message: 20:25:29.028: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o] ** Message: 20:25:29.028: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o ** Message: 20:25:29.040: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint] ** Message: 20:25:29.040: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 20:25:29.040: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 20:25:29.053: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation] ** Message: 20:25:29.059: Process optimal [Terminal [Segment("START"->"match"):[NER:affine:local:dna2dna]]] ** Message: 20:25:29.062: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:25:32.109: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:25:36.025: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:25:36.026: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:25:36.039: 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: 20:25:36.039: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:25:36.039: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:25:36.062: 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: 20:25:36.062: Process optimal [Terminal [Segment("match"->"END"):[NER:affine:local:dna2dna]]] ** Message: 20:25:36.064: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:25:38.094: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:25:40.421: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:25:40.421: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:25:40.433: 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: 20:25:40.434: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:25:40.434: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:25:40.446: 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: 20:25:40.446: Process optimal [HeuristicJoin:[Segment("match"->"match"):[NER:affine:local:dna2dna]]] ** Message: 20:25:40.450: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:25:46.818: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:26:00.619: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:26:00.620: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:26:00.633: 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: 20:26:00.633: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:26:00.633: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:26:00.646: 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: 20:26:00.646: Process optimal [Src span [Segment("match"->"ner"):[NER:affine:local:dna2dna]]] ** Message: 20:26:00.648: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:26:02.178: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:26:05.129: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:26:05.129: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:26:05.143: 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: 20:26:05.143: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:26:05.143: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:26:05.157: 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: 20:26:05.157: Process optimal [Src span traceback [Segment("match"->"ner"):[NER:affine:local:dna2dna]]] ** Message: 20:26:05.162: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:26:14.227: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:26:14.228: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:26:14.241: 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: 20:26:14.242: Process optimal [Dst span [Segment("ner"->"match"):[NER:affine:local:dna2dna]]] ** Message: 20:26:14.244: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:26:17.250: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:26:20.851: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:26:20.852: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:26:20.865: 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: 20:26:20.865: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:26:20.865: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:26:20.878: 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: 20:26:20.879: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.c ** Message: 20:26:21.431: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.c ** Message: 20:26:22.221: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.o] ** Message: 20:26:22.222: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.o ** Message: 20:26:22.237: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary] ** Message: 20:26:22.237: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.o] ** Message: 20:26:22.238: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.o ** Message: 20:26:22.252: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary] ** Message: 20:26:22.253: Bootstrapper processing model [NER:affine:local:protein2protein] ** Message: 20:26:22.253: Process optimal [optimal:NER:affine:local:protein2protein] ** Message: 20:26:22.254: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.c ** Message: 20:26:22.986: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.c ** Message: 20:26:23.965: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.c ** Message: 20:26:25.058: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.c ** Message: 20:26:27.438: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.c ** Message: 20:26:28.998: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.o] ** Message: 20:26:28.998: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.o ** Message: 20:26:29.012: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score] ** Message: 20:26:29.013: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.o] ** Message: 20:26:29.013: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.o ** Message: 20:26:29.027: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path] ** Message: 20:26:29.027: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.o] ** Message: 20:26:29.027: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.o ** Message: 20:26:29.041: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region] ** Message: 20:26:29.041: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o] ** Message: 20:26:29.041: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o ** Message: 20:26:29.055: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint] ** Message: 20:26:29.055: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o] ** Message: 20:26:29.055: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o ** Message: 20:26:29.069: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation] ** Message: 20:26:29.075: Process optimal [Terminal [Segment("START"->"match"):[NER:affine:local:protein2protein]]] ** Message: 20:26:29.077: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:26:30.643: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:26:33.685: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:26:33.686: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:26:33.700: 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: 20:26:33.700: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:26:33.700: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:26:33.715: 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: 20:26:33.715: Process optimal [Terminal [Segment("match"->"END"):[NER:affine:local:protein2protein]]] ** Message: 20:26:33.716: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:26:34.823: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:26:37.180: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:26:37.181: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:26:37.196: 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: 20:26:37.196: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:26:37.196: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:26:37.210: 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: 20:26:37.211: Process optimal [HeuristicJoin:[Segment("match"->"match"):[NER:affine:local:protein2protein]]] ** Message: 20:26:37.215: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:26:43.578: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:26:53.262: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:26:53.263: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:26:53.277: 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: 20:26:53.277: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:26:53.277: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:26:53.291: 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: 20:26:53.291: Process optimal [Src span [Segment("match"->"ner"):[NER:affine:local:protein2protein]]] ** Message: 20:26:53.293: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:26:55.034: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:26:57.765: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:26:57.766: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:26:57.780: 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: 20:26:57.780: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:26:57.780: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:26:57.794: 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: 20:26:57.795: Process optimal [Src span traceback [Segment("match"->"ner"):[NER:affine:local:protein2protein]]] ** Message: 20:26:57.799: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:27:03.689: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:27:03.690: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:27:03.704: 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: 20:27:03.704: Process optimal [Dst span [Segment("ner"->"match"):[NER:affine:local:protein2protein]]] ** Message: 20:27:03.706: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:27:05.638: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:27:09.230: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:27:09.231: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:27:09.245: 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: 20:27:09.245: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:27:09.245: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:27:09.259: 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: 20:27:09.260: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.c ** Message: 20:27:09.834: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.c ** Message: 20:27:10.461: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.o] ** Message: 20:27:10.462: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.o ** Message: 20:27:10.476: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary] ** Message: 20:27:10.476: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.o] ** Message: 20:27:10.476: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.o ** Message: 20:27:10.491: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary] ** Message: 20:27:10.491: Processing model [p2d] ** Message: 20:27:10.492: Bootstrapper processing model [protein2dna:local] ** Message: 20:27:10.492: Process optimal [optimal:protein2dna:local] ** Message: 20:27:10.493: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2dna_58_local_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2dna_58_local_32_find_32_score.c ** Message: 20:27:11.728: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2dna_58_local_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2dna_58_local_32_find_32_path.c ** Message: 20:27:13.609: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2dna_58_local_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2dna_58_local_32_find_32_region.c ** Message: 20:27:15.293: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2dna_58_local_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2dna_58_local_32_find_32_checkpoint.c ** Message: 20:27:19.276: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.c ** Message: 20:27:24.454: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2dna_58_local_32_find_32_score.o] ** Message: 20:27:24.454: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2dna_58_local_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2dna_58_local_32_find_32_score.o ** Message: 20:27:24.470: Adding function [optimal_58_protein2dna_58_local_32_find_32_score] ** Message: 20:27:24.470: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2dna_58_local_32_find_32_path.o] ** Message: 20:27:24.470: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2dna_58_local_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2dna_58_local_32_find_32_path.o ** Message: 20:27:24.485: Adding function [optimal_58_protein2dna_58_local_32_find_32_path] ** Message: 20:27:24.485: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2dna_58_local_32_find_32_region.o] ** Message: 20:27:24.486: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2dna_58_local_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2dna_58_local_32_find_32_region.o ** Message: 20:27:24.501: Adding function [optimal_58_protein2dna_58_local_32_find_32_region] ** Message: 20:27:24.501: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2dna_58_local_32_find_32_checkpoint.o] ** Message: 20:27:24.501: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2dna_58_local_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2dna_58_local_32_find_32_checkpoint.o ** Message: 20:27:24.516: Adding function [optimal_58_protein2dna_58_local_32_find_32_checkpoint] ** Message: 20:27:24.516: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.o] ** Message: 20:27:24.516: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.o ** Message: 20:27:24.532: Adding function [optimal_58_protein2dna_58_local_32_find_32_path_32_continuation] ** Message: 20:27:24.543: Process optimal [Terminal [Segment("START"->"match"):[protein2dna:local]]] ** Message: 20:27:24.547: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:27:29.585: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:27:39.369: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:27:39.369: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:27:39.404: 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: 20:27:39.405: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:27:39.405: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:27:39.419: 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: 20:27:39.419: Process optimal [Terminal [Segment("match"->"END"):[protein2dna:local]]] ** Message: 20:27:39.422: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:27:41.902: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:27:44.051: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:27:44.052: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:27:44.068: 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: 20:27:44.068: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:27:44.069: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:27:44.084: 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: 20:27:44.084: Process optimal [HeuristicJoin:[Segment("match"->"match"):[protein2dna:local]]] ** Message: 20:27:44.090: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:27:53.218: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:28:09.401: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:28:09.401: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:28:09.416: 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: 20:28:09.416: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:28:09.416: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:28:09.433: 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: 20:28:09.435: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.c ** Message: 20:28:10.357: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.c ** Message: 20:28:11.505: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.o] ** Message: 20:28:11.505: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.o ** Message: 20:28:11.522: Adding function [Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded] ** Message: 20:28:11.522: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.o] ** Message: 20:28:11.522: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.o ** Message: 20:28:11.538: Adding function [Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded] ** Message: 20:28:11.538: Processing model [p2d:b] ** Message: 20:28:11.539: Bootstrapper processing model [protein2dna:bestfit] ** Message: 20:28:11.539: Process optimal [optimal:protein2dna:bestfit] ** Message: 20:28:11.543: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2dna_58_bestfit_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2dna_58_bestfit_32_find_32_score.c ** Message: 20:28:16.509: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2dna_58_bestfit_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2dna_58_bestfit_32_find_32_path.c ** Message: 20:28:23.650: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2dna_58_bestfit_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2dna_58_bestfit_32_find_32_region.c ** Message: 20:28:30.555: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.c ** Message: 20:28:36.171: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.c ** Message: 20:28:41.441: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2dna_58_bestfit_32_find_32_score.o] ** Message: 20:28:41.441: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2dna_58_bestfit_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2dna_58_bestfit_32_find_32_score.o ** Message: 20:28:41.456: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_score] ** Message: 20:28:41.456: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2dna_58_bestfit_32_find_32_path.o] ** Message: 20:28:41.456: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2dna_58_bestfit_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2dna_58_bestfit_32_find_32_path.o ** Message: 20:28:41.473: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_path] ** Message: 20:28:41.473: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2dna_58_bestfit_32_find_32_region.o] ** Message: 20:28:41.473: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2dna_58_bestfit_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2dna_58_bestfit_32_find_32_region.o ** Message: 20:28:41.488: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_region] ** Message: 20:28:41.488: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.o] ** Message: 20:28:41.488: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.o ** Message: 20:28:41.504: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint] ** Message: 20:28:41.504: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.o] ** Message: 20:28:41.504: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.o ** Message: 20:28:41.520: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation] ** Message: 20:28:41.520: Processing model [p2g] ** Message: 20:28:41.521: Bootstrapper processing model [protein2genome:local] ** Message: 20:28:41.521: Process optimal [optimal:protein2genome:local] ** Message: 20:28:41.524: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2genome_58_local_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2genome_58_local_32_find_32_score.c ** Message: 20:28:45.337: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2genome_58_local_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2genome_58_local_32_find_32_path.c ** Message: 20:28:50.651: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2genome_58_local_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2genome_58_local_32_find_32_region.c ** Message: 20:28:53.960: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2genome_58_local_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2genome_58_local_32_find_32_checkpoint.c ** Message: 20:29:07.682: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.c ** Message: 20:29:25.243: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2genome_58_local_32_find_32_score.o] ** Message: 20:29:25.244: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2genome_58_local_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2genome_58_local_32_find_32_score.o ** Message: 20:29:25.259: Adding function [optimal_58_protein2genome_58_local_32_find_32_score] ** Message: 20:29:25.259: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2genome_58_local_32_find_32_path.o] ** Message: 20:29:25.260: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2genome_58_local_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2genome_58_local_32_find_32_path.o ** Message: 20:29:25.276: Adding function [optimal_58_protein2genome_58_local_32_find_32_path] ** Message: 20:29:25.276: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2genome_58_local_32_find_32_region.o] ** Message: 20:29:25.276: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2genome_58_local_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2genome_58_local_32_find_32_region.o ** Message: 20:29:25.292: Adding function [optimal_58_protein2genome_58_local_32_find_32_region] ** Message: 20:29:25.292: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2genome_58_local_32_find_32_checkpoint.o] ** Message: 20:29:25.293: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2genome_58_local_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2genome_58_local_32_find_32_checkpoint.o ** Message: 20:29:25.308: Adding function [optimal_58_protein2genome_58_local_32_find_32_checkpoint] ** Message: 20:29:25.308: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.o] ** Message: 20:29:25.309: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.o ** Message: 20:29:25.324: Adding function [optimal_58_protein2genome_58_local_32_find_32_path_32_continuation] ** Message: 20:29:25.396: Process optimal [Terminal [Segment("START"->"match"):[protein2genome:local]]] ** Message: 20:29:25.405: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:29:38.636: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:30:09.064: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:30:09.065: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:30:09.082: 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: 20:30:09.082: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:30:09.082: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:30:09.100: 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: 20:30:09.100: Process optimal [Terminal [Segment("match"->"END"):[protein2genome:local]]] ** Message: 20:30:09.105: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:30:15.861: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:30:28.762: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:30:28.763: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:30:28.780: 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: 20:30:28.780: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:30:28.780: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:30:28.797: 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: 20:30:28.797: Process optimal [HeuristicJoin:[Segment("match"->"match"):[protein2genome:local]]] ** Message: 20:30:28.809: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:30:51.434: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:31:57.295: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:31:57.296: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:31:57.313: 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: 20:31:57.313: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:31:57.313: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:31:57.336: 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: 20:31:57.336: Process optimal [Src span [Segment("match"->"intron 0:0 phase-T"):[protein2genome:local]]] ** Message: 20:31:57.341: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:32:04.851: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:32:12.305: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:32:12.306: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:32:12.324: 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: 20:32:12.324: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:32:12.324: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:32:12.342: 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: 20:32:12.342: Process optimal [Src span traceback [Segment("match"->"intron 0:0 phase-T"):[protein2genome:local]]] ** Message: 20:32:12.356: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:32:58.059: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:32:58.059: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:32:58.081: 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: 20:32:58.081: Process optimal [Dst span [Segment("intron 0:0 phase-T"->"match"):[protein2genome:local]]] ** Message: 20:32:58.089: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:33:23.631: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:33:56.589: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:33:56.589: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:33:56.608: 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: 20:33:56.609: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:33:56.609: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:33:56.628: 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: 20:33:56.629: Process optimal [Src span [Segment("match"->"intron 1:2 phase-T"):[protein2genome:local]]] ** Message: 20:33:56.633: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:34:02.678: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:34:13.993: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:34:13.993: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:34:14.012: 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: 20:34:14.013: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:34:14.013: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:34:14.043: 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: 20:34:14.043: Process optimal [Src span traceback [Segment("match"->"intron 1:2 phase-T"):[protein2genome:local]]] ** Message: 20:34:14.058: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:34:48.025: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:34:48.025: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:34:48.058: 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: 20:34:48.058: Process optimal [Dst span [Segment("intron 1:2 phase-T"->"match"):[protein2genome:local]]] ** Message: 20:34:48.066: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:35:02.817: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:35:37.271: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:35:37.273: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:35:37.297: 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: 20:35:37.297: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:35:37.297: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:35:37.318: 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: 20:35:37.318: Process optimal [Src span [Segment("match"->"intron 2:1 phase-T"):[protein2genome:local]]] ** Message: 20:35:37.323: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:35:47.844: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:35:58.375: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:35:58.375: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:35:58.394: 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: 20:35:58.395: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:35:58.395: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:35:58.416: 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: 20:35:58.416: Process optimal [Src span traceback [Segment("match"->"intron 2:1 phase-T"):[protein2genome:local]]] ** Message: 20:35:58.431: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:37:03.925: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:37:03.925: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:37:03.947: 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: 20:37:03.947: Process optimal [Dst span [Segment("intron 2:1 phase-T"->"match"):[protein2genome:local]]] ** Message: 20:37:03.956: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:37:25.251: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:37:54.701: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:37:54.702: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:37:54.722: 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: 20:37:54.722: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:37:54.722: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:37:54.743: 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: 20:37:54.745: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.c ** Message: 20:37:57.193: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.c ** Message: 20:37:58.817: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.o] ** Message: 20:37:58.818: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.o ** Message: 20:37:58.838: Adding function [Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary] ** Message: 20:37:58.838: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.o] ** Message: 20:37:58.838: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.o ** Message: 20:37:58.858: Adding function [Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary] ** Message: 20:37:58.867: Processing model [p2g:b] ** Message: 20:37:58.868: Bootstrapper processing model [protein2genome:bestfit] ** Message: 20:37:58.868: Process optimal [optimal:protein2genome:bestfit] ** Message: 20:37:58.878: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2genome_58_bestfit_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2genome_58_bestfit_32_find_32_score.c ** Message: 20:38:17.771: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2genome_58_bestfit_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2genome_58_bestfit_32_find_32_path.c ** Message: 20:38:40.038: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2genome_58_bestfit_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2genome_58_bestfit_32_find_32_region.c ** Message: 20:38:57.285: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.c ** Message: 20:39:05.563: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.c ** Message: 20:39:25.281: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2genome_58_bestfit_32_find_32_score.o] ** Message: 20:39:25.283: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2genome_58_bestfit_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2genome_58_bestfit_32_find_32_score.o ** Message: 20:39:25.303: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_score] ** Message: 20:39:25.303: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2genome_58_bestfit_32_find_32_path.o] ** Message: 20:39:25.303: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2genome_58_bestfit_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2genome_58_bestfit_32_find_32_path.o ** Message: 20:39:25.323: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_path] ** Message: 20:39:25.323: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2genome_58_bestfit_32_find_32_region.o] ** Message: 20:39:25.323: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2genome_58_bestfit_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2genome_58_bestfit_32_find_32_region.o ** Message: 20:39:25.344: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_region] ** Message: 20:39:25.344: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.o] ** Message: 20:39:25.344: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.o ** Message: 20:39:25.365: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint] ** Message: 20:39:25.365: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.o] ** Message: 20:39:25.365: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.o ** Message: 20:39:25.387: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation] ** Message: 20:39:25.388: Processing model [c2c] ** Message: 20:39:25.389: Bootstrapper processing model [coding2coding] ** Message: 20:39:25.389: Process optimal [optimal:coding2coding] ** Message: 20:39:25.392: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_coding2coding_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_coding2coding_32_find_32_score.c ** Message: 20:39:27.819: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_coding2coding_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_coding2coding_32_find_32_path.c ** Message: 20:39:31.294: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_coding2coding_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_coding2coding_32_find_32_region.c ** Message: 20:39:34.717: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_coding2coding_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_coding2coding_32_find_32_checkpoint.c ** Message: 20:39:44.242: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_coding2coding_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_coding2coding_32_find_32_path_32_continuation.c ** Message: 20:39:57.642: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_coding2coding_32_find_32_score.o] ** Message: 20:39:57.642: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_coding2coding_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_coding2coding_32_find_32_score.o ** Message: 20:39:57.665: Adding function [optimal_58_coding2coding_32_find_32_score] ** Message: 20:39:57.665: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_coding2coding_32_find_32_path.o] ** Message: 20:39:57.665: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_coding2coding_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_coding2coding_32_find_32_path.o ** Message: 20:39:57.687: Adding function [optimal_58_coding2coding_32_find_32_path] ** Message: 20:39:57.690: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_coding2coding_32_find_32_region.o] ** Message: 20:39:57.691: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_coding2coding_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_coding2coding_32_find_32_region.o ** Message: 20:39:57.712: Adding function [optimal_58_coding2coding_32_find_32_region] ** Message: 20:39:57.712: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_coding2coding_32_find_32_checkpoint.o] ** Message: 20:39:57.712: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_coding2coding_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_coding2coding_32_find_32_checkpoint.o ** Message: 20:39:57.734: Adding function [optimal_58_coding2coding_32_find_32_checkpoint] ** Message: 20:39:57.734: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_coding2coding_32_find_32_path_32_continuation.o] ** Message: 20:39:57.734: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_coding2coding_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_coding2coding_32_find_32_path_32_continuation.o ** Message: 20:39:57.756: Adding function [optimal_58_coding2coding_32_find_32_path_32_continuation] ** Message: 20:39:57.793: Process optimal [Terminal [Segment("START"->"match"):[coding2coding]]] ** Message: 20:39:57.801: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:40:06.731: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:40:46.015: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:40:46.015: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:40:46.037: 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: 20:40:46.037: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:40:46.037: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:40:46.058: 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: 20:40:46.058: Process optimal [Terminal [Segment("match"->"END"):[coding2coding]]] ** Message: 20:40:46.062: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:40:50.495: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:40:57.335: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:40:57.336: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:40:57.357: 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: 20:40:57.358: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:40:57.358: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:40:57.379: 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: 20:40:57.379: Process optimal [HeuristicJoin:[Segment("match"->"match"):[coding2coding]]] ** Message: 20:40:57.391: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:41:24.513: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:42:24.034: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:42:24.035: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:42:24.057: 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: 20:42:24.057: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:42:24.057: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/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: 20:42:24.079: 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: 20:42:24.081: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.c ** Message: 20:42:24.585: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.c ** Message: 20:42:25.533: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.o] ** Message: 20:42:25.533: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.o ** Message: 20:42:25.556: Adding function [Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded] ** Message: 20:42:25.556: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.o] ** Message: 20:42:25.556: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.o ** Message: 20:42:25.579: Adding function [Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded] ** Message: 20:42:25.580: Processing model [c2g] ** Message: 20:42:25.582: Bootstrapper processing model [coding2genome] ** Message: 20:42:25.582: Process optimal [optimal:coding2genome] ** Message: 20:42:25.588: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_coding2genome_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_coding2genome_32_find_32_score.c ** Message: 20:42:33.790: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_coding2genome_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_coding2genome_32_find_32_path.c ** Message: 20:42:42.200: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_coding2genome_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_coding2genome_32_find_32_region.c ** Message: 20:42:52.640: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_coding2genome_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_coding2genome_32_find_32_checkpoint.c ** Message: 20:43:29.295: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_coding2genome_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_coding2genome_32_find_32_path_32_continuation.c ** Message: 20:45:00.317: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_coding2genome_32_find_32_score.o] ** Message: 20:45:00.317: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_coding2genome_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_coding2genome_32_find_32_score.o ** Message: 20:45:00.340: Adding function [optimal_58_coding2genome_32_find_32_score] ** Message: 20:45:00.341: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_coding2genome_32_find_32_path.o] ** Message: 20:45:00.341: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_coding2genome_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_coding2genome_32_find_32_path.o ** Message: 20:45:00.363: Adding function [optimal_58_coding2genome_32_find_32_path] ** Message: 20:45:00.363: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_coding2genome_32_find_32_region.o] ** Message: 20:45:00.363: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_coding2genome_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_coding2genome_32_find_32_region.o ** Message: 20:45:00.386: Adding function [optimal_58_coding2genome_32_find_32_region] ** Message: 20:45:00.386: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_coding2genome_32_find_32_checkpoint.o] ** Message: 20:45:00.386: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_coding2genome_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_coding2genome_32_find_32_checkpoint.o ** Message: 20:45:00.410: Adding function [optimal_58_coding2genome_32_find_32_checkpoint] ** Message: 20:45:00.410: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_coding2genome_32_find_32_path_32_continuation.o] ** Message: 20:45:00.410: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_coding2genome_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_coding2genome_32_find_32_path_32_continuation.o ** Message: 20:45:00.435: Adding function [optimal_58_coding2genome_32_find_32_path_32_continuation] ** Message: 20:45:00.437: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.c ** Message: 20:45:01.756: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.c ** Message: 20:45:03.914: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.o] ** Message: 20:45:03.914: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.o ** Message: 20:45:03.938: Adding function [Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary] ** Message: 20:45:03.938: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.o] ** Message: 20:45:03.938: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.o ** Message: 20:45:03.961: Adding function [Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary] ** Message: 20:45:03.962: Processing model [cd2g] ** Message: 20:45:03.964: Bootstrapper processing model [cdna2genome] ** Message: 20:45:03.964: Process optimal [optimal:cdna2genome] ** Message: 20:45:03.976: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_cdna2genome_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_cdna2genome_32_find_32_score.c ** Message: 20:45:29.742: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_cdna2genome_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_cdna2genome_32_find_32_path.c ** Message: 20:46:21.967: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_cdna2genome_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_cdna2genome_32_find_32_region.c ** Message: 20:46:53.324: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_cdna2genome_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_cdna2genome_32_find_32_checkpoint.c ** Message: 20:50:32.979: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_cdna2genome_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_cdna2genome_32_find_32_path_32_continuation.c ** Message: 20:55:15.941: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_cdna2genome_32_find_32_score.o] ** Message: 20:55:15.941: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_cdna2genome_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_cdna2genome_32_find_32_score.o ** Message: 20:55:15.976: Adding function [optimal_58_cdna2genome_32_find_32_score] ** Message: 20:55:15.976: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_cdna2genome_32_find_32_path.o] ** Message: 20:55:15.977: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_cdna2genome_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_cdna2genome_32_find_32_path.o ** Message: 20:55:16.002: Adding function [optimal_58_cdna2genome_32_find_32_path] ** Message: 20:55:16.020: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_cdna2genome_32_find_32_region.o] ** Message: 20:55:16.020: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_cdna2genome_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_cdna2genome_32_find_32_region.o ** Message: 20:55:16.045: Adding function [optimal_58_cdna2genome_32_find_32_region] ** Message: 20:55:16.045: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_cdna2genome_32_find_32_checkpoint.o] ** Message: 20:55:16.045: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_cdna2genome_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_cdna2genome_32_find_32_checkpoint.o ** Message: 20:55:16.070: Adding function [optimal_58_cdna2genome_32_find_32_checkpoint] ** Message: 20:55:16.071: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_cdna2genome_32_find_32_path_32_continuation.o] ** Message: 20:55:16.071: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_cdna2genome_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/optimal_58_cdna2genome_32_find_32_path_32_continuation.o ** Message: 20:55:16.097: Adding function [optimal_58_cdna2genome_32_find_32_path_32_continuation] ** Message: 20:55:16.099: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.c ** Message: 20:55:18.493: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.c ** Message: 20:55:21.037: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o] ** Message: 20:55:21.037: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o ** Message: 20:55:21.065: Adding function [Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary] ** Message: 20:55:21.066: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o] ** Message: 20:55:21.066: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly6_46_1/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o ** Message: 20:55:21.091: Adding function [Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary] ** Message: 20:55:21.092: Compiling with: [cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -o c4_model_lookup.o -c c4_model_lookup.c] ** Message: 20:55:21.579: Adding: [c4_model_lookup.o] ** Message: 20:55:21.579: Adding object file [c4_model_lookup.o] to archive ar -Sq c4_model_archive.a c4_model_lookup.o ** Message: 20:55:21.605: Indexing archive [c4_model_archive.a] ranlib c4_model_archive.a ** Message: 20:55:21.673: Done ** Message: 20:55:21.673: Finished building bootstrapping components cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/hub -I../../src/general -DHOSTTYPE="\"x86_64-portbld-dragonfly6.1\"" -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I. -DUSE_COMPILED_MODELS -c ../../src/c4/viterbi.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/hub -I../../src/general -DHOSTTYPE="\"x86_64-portbld-dragonfly6.1\"" -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I. -DUSE_COMPILED_MODELS -c ../../src/sdp/scheduler.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o exonerate exonerate.o viterbi.o scheduler.o c4_model_archive.a ../../src/comparison/wordhood.o ../../src/comparison/hspset.o ../../src/comparison/seeder.o ../../src/comparison/comparison.o ../../src/database/fastapipe.o ../../src/database/fastadb.o ../../src/struct/dejavu.o ../../src/struct/fsm.o ../../src/struct/vfsm.o ../../src/struct/sparsecache.o ../../src/hub/gam.o ../../src/hub/bsam.o ../../src/hub/analysis.o ../../src/general/compoundfile.o ../../src/general/threadref.o ../../src/c4/c4.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/opair.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/layout.o ../../src/c4/region.o ../../src/c4/subopt.o ../../src/bsdp/bsdp.o ../../src/bsdp/sar.o ../../src/bsdp/heuristic.o ../../src/bsdp/hpair.o ../../src/sdp/boundary.o ../../src/sdp/sdp.o ../../src/sdp/lookahead.o ../../src/sdp/straceback.o ../../src/struct/matrix.o ../../src/struct/slist.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/translate.o ../../src/sequence/splice.o ../../src/model/affine.o ../../src/model/est2genome.o ../../src/model/ner.o ../../src/model/protein2dna.o ../../src/model/protein2genome.o ../../src/model/coding2coding.o ../../src/model/coding2genome.o ../../src/model/cdna2genome.o ../../src/model/genome2genome.o ../../src/model/ungapped.o ../../src/model/intron.o ../../src/model/frameshift.o ../../src/model/phase.o ../../src/model/modeltype.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/socket.o ../../src/general/jobqueue.o ../../src/comparison/match.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/hub -I../../src/general -DHOSTTYPE="\"x86_64-portbld-dragonfly6.1\"" -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c ipcress.c ipcress.c: In function 'Ipcress_prepare_PCR': ipcress.c:264:9: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] g_strup(primer_a); ^~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:82, from ipcress.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here gchar* g_strup (gchar *string); ^~~~~~~ ipcress.c:265:9: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] g_strup(primer_b); ^~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:82, from ipcress.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here gchar* g_strup (gchar *string); ^~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o ipcress ipcress.o ../../src/comparison/pcr.o ../../src/comparison/wordhood.o ../../src/database/fastadb.o ../../src/sequence/alphabet.o ../../src/sequence/sequence.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/struct/fsm.o ../../src/struct/slist.o ../../src/struct/matrix.o ../../src/struct/recyclebin.o ../../src/struct/sparsecache.o ../../src/general/lineparse.o ../../src/general/argument.o ../../src/general/compoundfile.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/hub -I../../src/general -DHOSTTYPE="\"x86_64-portbld-dragonfly6.1\"" -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c exonerate-server.c exonerate-server.c: In function 'Exonerate_Server_get_hsps': exonerate-server.c:349:13: warning: Deprecated pre-processor symbol, replace with 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_sprintfa(str, " %d %d %d", ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ exonerate-server.c:357:13: warning: Deprecated pre-processor symbol, replace with g_string_sprintfa(str, "\n"); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o exonerate-server exonerate-server.o ../../src/general/socket.o ../../src/general/argument.o ../../src/comparison/hspset.o ../../src/comparison/match.o ../../src/comparison/wordhood.o ../../src/database/dataset.o ../../src/database/index.o ../../src/database/fastadb.o ../../src/struct/bitarray.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/struct/splaytree.o ../../src/struct/noitree.o ../../src/struct/vfsm.o ../../src/struct/pqueue.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/translate.o ../../src/sequence/splice.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl Making all in util cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastaclean.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastaclean fastaclean.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastaclip.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastaclip fastaclip.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastachecksum.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastachecksum fastachecksum.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastacomposition.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastacomposition fastacomposition.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastadiff.c fastadiff.c: In function 'fasta_diff': fastadiff.c:70:13: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] comp = g_strcasecmp; ^~~~ In file included from /usr/local/include/glib-2.0/glib.h:82, from ../../src/general/argument.h:26, from fastadiff.c:19: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastadiff fastadiff.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastaexplode.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastaexplode fastaexplode.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastafetch.c fastafetch.c: In function 'get_query_list': fastafetch.c:121:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(query, "stdin")){ ^~ In file included from /usr/local/include/glib-2.0/glib.h:82, from ../../src/general/argument.h:26, from fastafetch.c:21: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastafetch fastafetch.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastahardmask.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastahardmask fastahardmask.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastaindex.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastaindex fastaindex.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastalength.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastalength fastalength.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastanrdb.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastanrdb fastanrdb.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastaoverlap.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastaoverlap fastaoverlap.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastareformat.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastareformat fastareformat.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastaremove.c fastaremove.c: In function 'Argument_main': fastaremove.c:73:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(remove_path, "stdin")){ ^~ In file included from /usr/local/include/glib-2.0/glib.h:82, from ../../src/general/argument.h:26, from fastaremove.c:19: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastaremove fastaremove.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastarevcomp.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastarevcomp fastarevcomp.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastasoftmask.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastasoftmask fastasoftmask.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastasort.c fastasort.c: In function 'SortKey_Mask_create': fastasort.c:130:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(sort_key, "id")) ^~ In file included from /usr/local/include/glib-2.0/glib.h:82, from ../../src/general/argument.h:26, from fastasort.c:20: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ fastasort.c:132:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] else if(!g_strcasecmp(sort_key, "len")) ^~~~ In file included from /usr/local/include/glib-2.0/glib.h:82, from ../../src/general/argument.h:26, from fastasort.c:20: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ fastasort.c:134:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] else if(!g_strcasecmp(sort_key, "seq")) ^~~~ In file included from /usr/local/include/glib-2.0/glib.h:82, from ../../src/general/argument.h:26, from fastasort.c:20: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastasort fastasort.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastasplit.c fastasplit.c: In function 'Argument_main': fastasplit.c:92:13: warning: 'g_basename' is deprecated: Use 'g_path_get_basename' instead [-Wdeprecated-declarations] output_dir, G_DIR_SEPARATOR, g_basename(query_path)); ^~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:48, from ../../src/general/argument.h:26, from fastasplit.c:20: /usr/local/include/glib-2.0/glib/gfileutils.h:205:14: note: declared here const gchar *g_basename (const gchar *file_name); ^~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastasplit fastasplit.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastasubseq.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastasubseq fastasubseq.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastatranslate.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastatranslate fastatranslate.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastavalidcds.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastavalidcds fastavalidcds.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fasta2esd.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fasta2esd fasta2esd.o ../../src/database/dataset.o ../../src/struct/bitarray.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastaannotatecdna.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastaannotatecdna fastaannotatecdna.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c esd2esi.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o esd2esi esd2esi.o ../../src/database/dataset.o ../../src/database/index.o ../../src/general/threadref.o ../../src/struct/bitarray.o ../../src/struct/vfsm.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/struct/noitree.o ../../src/struct/splaytree.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/comparison/wordhood.o ../../src/comparison/hspset.o ../../src/comparison/match.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl Making all in test Making all in data Making all in cdna Making all in protein Making all in exonerate Making all in ipcress Making all in util SUCCEEDED 00:36:35 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for exonerate-2.4.0 ===> Generating temporary packing list Making install in doc Making install in man Making install in man1 /usr/bin/make install-man1 /bin/sh ../../../mkinstalldirs /construction/biology/exonerate/stage/usr/local/man/man1 install -m 0644 ./exonerate.1 /construction/biology/exonerate/stage/usr/local/man/man1/exonerate.1 install -m 0644 ./ipcress.1 /construction/biology/exonerate/stage/usr/local/man/man1/ipcress.1 install -m 0644 ./exonerate-server.1 /construction/biology/exonerate/stage/usr/local/man/man1/exonerate-server.1 install -m 0644 ./fastautils.1 /construction/biology/exonerate/stage/usr/local/man/man1/fastautils.1 Making install in src Making install in struct Making install in general Making install in sequence Making install in comparison Making install in database Making install in c4 Making install in bsdp Making install in sdp Making install in model Making install in hub Making install in program /bin/sh ../../mkinstalldirs /construction/biology/exonerate/stage/usr/local/bin install -s -m 555 exonerate /construction/biology/exonerate/stage/usr/local/bin/exonerate install -s -m 555 ipcress /construction/biology/exonerate/stage/usr/local/bin/ipcress install -s -m 555 exonerate-server /construction/biology/exonerate/stage/usr/local/bin/exonerate-server Making install in util /bin/sh ../../mkinstalldirs /construction/biology/exonerate/stage/usr/local/bin install -s -m 555 fastaclean /construction/biology/exonerate/stage/usr/local/bin/fastaclean install -s -m 555 fastaclip /construction/biology/exonerate/stage/usr/local/bin/fastaclip install -s -m 555 fastachecksum /construction/biology/exonerate/stage/usr/local/bin/fastachecksum install -s -m 555 fastacomposition /construction/biology/exonerate/stage/usr/local/bin/fastacomposition install -s -m 555 fastadiff /construction/biology/exonerate/stage/usr/local/bin/fastadiff install -s -m 555 fastaexplode /construction/biology/exonerate/stage/usr/local/bin/fastaexplode install -s -m 555 fastafetch /construction/biology/exonerate/stage/usr/local/bin/fastafetch install -s -m 555 fastahardmask /construction/biology/exonerate/stage/usr/local/bin/fastahardmask install -s -m 555 fastaindex /construction/biology/exonerate/stage/usr/local/bin/fastaindex install -s -m 555 fastalength /construction/biology/exonerate/stage/usr/local/bin/fastalength install -s -m 555 fastanrdb /construction/biology/exonerate/stage/usr/local/bin/fastanrdb install -s -m 555 fastaoverlap /construction/biology/exonerate/stage/usr/local/bin/fastaoverlap install -s -m 555 fastareformat /construction/biology/exonerate/stage/usr/local/bin/fastareformat install -s -m 555 fastaremove /construction/biology/exonerate/stage/usr/local/bin/fastaremove install -s -m 555 fastarevcomp /construction/biology/exonerate/stage/usr/local/bin/fastarevcomp install -s -m 555 fastasoftmask /construction/biology/exonerate/stage/usr/local/bin/fastasoftmask install -s -m 555 fastasort /construction/biology/exonerate/stage/usr/local/bin/fastasort install -s -m 555 fastasplit /construction/biology/exonerate/stage/usr/local/bin/fastasplit install -s -m 555 fastasubseq /construction/biology/exonerate/stage/usr/local/bin/fastasubseq install -s -m 555 fastatranslate /construction/biology/exonerate/stage/usr/local/bin/fastatranslate install -s -m 555 fastavalidcds /construction/biology/exonerate/stage/usr/local/bin/fastavalidcds install -s -m 555 fasta2esd /construction/biology/exonerate/stage/usr/local/bin/fasta2esd install -s -m 555 fastaannotatecdna /construction/biology/exonerate/stage/usr/local/bin/fastaannotatecdna install -s -m 555 esd2esi /construction/biology/exonerate/stage/usr/local/bin/esd2esi Making install in test Making install in data Making install in cdna Making install in protein Making install in exonerate Making install in ipcress Making install in util ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:03 ------------------------------------------------------------------------------- -- Phase: check-plist ------------------------------------------------------------------------------- ====> Checking for pkg-plist issues (check-plist) ===> Parsing plist ===> Checking for items in STAGEDIR missing from pkg-plist ===> Checking for items in pkg-plist which are not in STAGEDIR ===> No pkg-plist issues found (check-plist) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for exonerate-2.4.0 file sizes/checksums [31]: 0% file sizes/checksums [31]: 100% packing files [31]: 0% packing files [31]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:22 TOTAL TIME 00:37:29