=> Building biology/exonerate Started : Wednesday, 24 JUL 2019 at 16:51:50 UTC Platform: 5.7-DEVELOPMENT DragonFly v5.7.0.83.g49866-DEVELOPMENT #40: Sun Jun 30 03:00:04 PDT 2019 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.6-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.6-SYNTH UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 TERM=dumb PKG_CACHEDIR=/var/cache/pkg8 PKG_DBDIR=/var/db/pkg8 PORTSDIR=/xports LANG=C HOME=/root USER=root -------------------------------------------------- -- Options -------------------------------------------------- -------------------------------------------------- -- 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 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} -------------------------------------------------- -- 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" -------------------------------------------------- -- MAKE_ARGS -------------------------------------------------- DESTDIR=/construction/biology/exonerate/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- GTK2_VERSION="2.10.0" GTK3_VERSION="3.0.0" OSREL=5.6 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" -------------------------------------------------- -- 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 -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=Release-5.6 USE_PACKAGE_DEPENDS_ONLY=yes PACKAGE_BUILDING=yes BATCH=yes PKG_CREATE_VERBOSE=yes PORTSDIR=/xports DISTDIR=/distfiles WRKDIRPREFIX=/construction PORT_DBDIR=/options PACKAGES=/packages MAKE_JOBS_NUMBER_LIMIT=5 LICENSES_ACCEPTED= NONE HAVE_COMPAT_IA32_KERN= CONFIGURE_MAX_CMD_LEN=262144 _PERL5_FROM_BIN=5.28.1 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=8 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500601 OSVERSION=9999999 OSREL=5.6 _OSRELEASE=5.6-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> exonerate-2.4.0 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.11.1.txz Installing pkg-1.11.1... Extracting pkg-1.11.1: .......... done ===> exonerate-2.4.0 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of exonerate-2.4.0 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by exonerate-2.4.0 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by exonerate-2.4.0 for building => SHA256 Checksum OK for exonerate-2.4.0.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user ===> 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. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for exonerate-2.4.0 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> exonerate-2.4.0 depends on package: pkgconf>=1.3.0_1 - not found ===> Installing existing package /packages/All/pkgconf-1.6.1,1.txz Installing pkgconf-1.6.1,1... Extracting pkgconf-1.6.1,1: .......... done ===> exonerate-2.4.0 depends on package: pkgconf>=1.3.0_1 - found ===> Returning to build of exonerate-2.4.0 -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- ===> exonerate-2.4.0 depends on shared library: libglib-2.0.so - not found ===> Installing existing package /packages/All/glib-2.56.3_5,1.txz Installing glib-2.56.3_5,1... `-- Installing gettext-runtime-0.20.1... | `-- Installing indexinfo-0.3.1... | `-- Extracting indexinfo-0.3.1: .... done `-- Extracting gettext-runtime-0.20.1: .......... done `-- Installing libffi-3.2.1_3... `-- Extracting libffi-3.2.1_3: .......... done `-- Installing libiconv-1.14_11... `-- Extracting libiconv-1.14_11: .......... done `-- Installing libxml2-2.9.9... `-- Extracting libxml2-2.9.9: .......... done `-- Installing pcre-8.43_1... `-- Extracting pcre-8.43_1: .......... done `-- Installing python36-3.6.9... | `-- Installing expat-2.2.6_1... | `-- Extracting expat-2.2.6_1: .......... done | `-- Installing libressl-2.9.2... | `-- Extracting libressl-2.9.2: .......... done | `-- Installing ncurses-6.1.20190525... | `-- Extracting ncurses-6.1.20190525: .......... done | `-- Installing readline-8.0.0... | `-- Extracting readline-8.0.0: .......... done `-- Extracting python36-3.6.9: .......... done Extracting glib-2.56.3_5,1: .......... done No schema files found: doing nothing. Message from python36-3.6.9: =========================================================================== Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py36-gdbm databases/py-gdbm@py36 py36-sqlite3 databases/py-sqlite3@py36 py36-tkinter x11-toolkits/py-tkinter@py36 =========================================================================== ===> exonerate-2.4.0 depends on shared library: libglib-2.0.so - found (/usr/local/lib/libglib-2.0.so) ===> Returning to build of exonerate-2.4.0 ===> exonerate-2.4.0 depends on shared library: libintl.so - found (/usr/local/lib/libintl.so) -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for exonerate-2.4.0 configure: loading site script /xports/Templates/config.site checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking whether make sets $(MAKE)... yes checking for working aclocal-1.4... missing checking for working autoconf... missing checking for working automake-1.4... missing checking for working autoheader... missing checking for working makeinfo... missing checking for gcc... cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for a BSD-compatible install... /usr/bin/install -c checking whether make sets $(MAKE)... (cached) yes checking for an ANSI C-conforming const... yes checking for inline... inline checking how to run the C preprocessor... cpp checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep checking for ANSI C header files... (cached) yes checking for sys/types.h... (cached) yes checking for sys/stat.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for memory.h... (cached) yes checking for strings.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for unistd.h... (cached) yes checking for limits.h... (cached) yes checking for errno.h... (cached) yes checking for math.h... (cached) yes checking for strings.h... (cached) yes checking for ctype.h... (cached) yes checking for sys/stat.h... (cached) yes checking for sys/types.h... (cached) yes checking for time.h... (cached) yes checking for unistd.h... (cached) yes checking build system type... x86_64-portbld-dragonfly5.6 checking host system type... x86_64-portbld-dragonfly5.6 Set host to x86_64-portbld-dragonfly5.6 x86_64-portbld-dragonfly5.6 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 -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for exonerate-2.4.0 Making all in doc Making all in man Making all in man1 Making all in src Making all in struct cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fsm.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fsm.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c recyclebin.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fsm.test fsm.test.o fsm.o recyclebin.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c matrix.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c matrix.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o matrix.test matrix.test.o matrix.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c pqueue.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c pqueue.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o pqueue.test pqueue.test.o pqueue.o recyclebin.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c slist.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c slist.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o slist.test slist.test.o slist.o recyclebin.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c rangetree.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c rangetree.c rangetree.c: In function 'RangeTree_insert_recent': rangetree.c:151:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] g_tree_traverse(rt->recent_data, RangeTree_insert_recent_collect, ^~~~~~~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:88, from rangetree.h:23, from rangetree.c:18: /usr/local/include/glib-2.0/glib/gtree.h:88:10: note: declared here void g_tree_traverse (GTree *tree, ^~~~~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o rangetree.test rangetree.test.o rangetree.o recyclebin.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c vfsm.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c vfsm.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o vfsm.test vfsm.test.o vfsm.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c recyclebin.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o recyclebin.test recyclebin.test.o recyclebin.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c sparsecache.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c sparsecache.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o sparsecache.test sparsecache.test.o sparsecache.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c dejavu.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c dejavu.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o dejavu.test dejavu.test.o dejavu.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c bitarray.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c bitarray.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o bitarray.test bitarray.test.o bitarray.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c splaytree.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c splaytree.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o splaytree.test splaytree.test.o splaytree.o recyclebin.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c noitree.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c noitree.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o noitree.test noitree.test.o noitree.o recyclebin.o splaytree.o -L/usr/local/lib -lglib-2.0 -lintl Making all in general cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c argument.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c argument.c argument.c: In function 'ArgumentParse_boolean': argument.c:138:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(arg_string, true_string[i])) ^~ In file included from /usr/local/include/glib-2.0/glib.h:79, from argument.h:26, from argument.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ argument.c:140:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(arg_string, false_string[i])) ^~ In file included from /usr/local/include/glib-2.0/glib.h:79, from argument.h:26, from argument.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ argument.c: In function 'main': argument.c:307:9: warning: 'g_thread_init' is deprecated [-Wdeprecated-declarations] g_thread_init(NULL); ^~~~~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:108, from argument.h:26, from argument.c:16: /usr/local/include/glib-2.0/glib/deprecated/gthread.h:265:10: note: declared here void g_thread_init (gpointer vtable); ^~~~~~~~~~~~~ argument.c: In function 'Argument_process': argument.c:502:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] g_tree_traverse(arg->option_registry, Argument_set_env_var_func, ^~~~~~~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:88, from argument.h:26, from argument.c:16: /usr/local/include/glib-2.0/glib/gtree.h:88:10: note: declared here void g_tree_traverse (GTree *tree, ^~~~~~~~~~~~~~~ argument.c:559:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] g_tree_traverse(arg->option_registry, ^~~~~~~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:88, from argument.h:26, from argument.c:16: /usr/local/include/glib-2.0/glib/gtree.h:88:10: note: declared here void g_tree_traverse (GTree *tree, ^~~~~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o argument.test argument.test.o argument.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c lineparse.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c lineparse.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o lineparse.test lineparse.test.o lineparse.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c compoundfile.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c compoundfile.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o compoundfile.test compoundfile.test.o compoundfile.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c socket.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c socket.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o socket.test socket.test.o socket.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c jobqueue.test.c jobqueue.test.c: In function 'main': jobqueue.test.c:35:9: warning: 'g_thread_init' is deprecated [-Wdeprecated-declarations] g_thread_init(NULL); ^~~~~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:108, from jobqueue.h:23, from jobqueue.test.c:17: /usr/local/include/glib-2.0/glib/deprecated/gthread.h:265:10: note: declared here void g_thread_init (gpointer vtable); ^~~~~~~~~~~~~ cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c jobqueue.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o jobqueue.test jobqueue.test.o jobqueue.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c threadref.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c threadref.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o threadref.test threadref.test.o threadref.o -lpthread -L/usr/local/lib -lglib-2.0 -lintl Making all in sequence cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c sequence.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c sequence.c sequence.c: In function 'Sequence_destroy_annotation_tree': sequence.c:97:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] g_tree_traverse(tree, Sequence_destroy_annotation_data, ^~~~~~~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:88, from sequence.h:24, from sequence.c:21: /usr/local/include/glib-2.0/glib/gtree.h:88:10: note: declared here void g_tree_traverse (GTree *tree, ^~~~~~~~~~~~~~~ cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c alphabet.c alphabet.c: In function 'Alphabet_name_get_type': alphabet.c:317:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(name, dna_string[i])) ^~ In file included from /usr/local/include/glib-2.0/glib.h:79, from alphabet.h:24, from alphabet.c:19: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ alphabet.c:320:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(name, protein_string[i])) ^~ In file included from /usr/local/include/glib-2.0/glib.h:79, from alphabet.h:24, from alphabet.c:19: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ alphabet.c:323:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(name, unknown_string[i])) ^~ In file included from /usr/local/include/glib-2.0/glib.h:79, from alphabet.h:24, from alphabet.c:19: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c translate.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c splice.c splice.c: In function 'SplicePredictor_parse_data': splice.c:146:17: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(word, "splice")) ^~ In file included from /usr/local/include/glib-2.0/glib.h:79, from splice.h:23, from splice.c:22: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ splice.c: In function 'SplicePredictor_add_5SS_data': splice.c:195:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if((!path) || (!strlen(path)) || (!g_strcasecmp(path, "primate"))) ^~ In file included from /usr/local/include/glib-2.0/glib.h:79, from splice.h:23, from splice.c:22: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ splice.c: In function 'SplicePredictor_add_3SS_data': splice.c:203:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if((!path) || (!strlen(path)) || (!g_strcasecmp(path, "primate"))) ^~ In file included from /usr/local/include/glib-2.0/glib.h:79, from splice.h:23, from splice.c:22: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o sequence.test sequence.test.o sequence.o alphabet.o translate.o splice.o ../../src/struct/matrix.o ../../src/struct/sparsecache.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c submat.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c submat.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o submat.test submat.test.o submat.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c translate.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o translate.test translate.test.o translate.o ../../src/general/argument.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c splice.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o splice.test splice.test.o splice.o ../../src/struct/matrix.o ../../src/struct/sparsecache.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c alphabet.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o alphabet.test alphabet.test.o alphabet.o ../../src/general/argument.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c codonsubmat.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c codonsubmat.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o codonsubmat.test codonsubmat.test.o codonsubmat.o ../../src/general/argument.o -lm -L/usr/local/lib -lglib-2.0 -lintl Making all in comparison cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c wordhood.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c wordhood.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o wordhood.test wordhood.test.o wordhood.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c hspset.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c hspset.c hspset.c: In function 'HSP_Display_insert': hspset.c:637:9: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] g_strdown(query_str); ^~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:79, from hspset.h:26, from hspset.c:20: /usr/local/include/glib-2.0/glib/gstrfuncs.h:208:23: note: declared here gchar* g_strdown (gchar *string); ^~~~~~~~~ hspset.c:638:9: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] g_strdown(target_str); ^~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:79, from hspset.h:26, from hspset.c:20: /usr/local/include/glib-2.0/glib/gstrfuncs.h:208:23: note: declared here gchar* g_strdown (gchar *string); ^~~~~~~~~ hspset.c:640:9: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] g_strup(query_str); ^~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:79, from hspset.h:26, from hspset.c:20: /usr/local/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here gchar* g_strup (gchar *string); ^~~~~~~ hspset.c:641:9: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] g_strup(target_str); ^~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:79, from hspset.h:26, from hspset.c:20: /usr/local/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here gchar* g_strup (gchar *string); ^~~~~~~ cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c match.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o hspset.test hspset.test.o hspset.o match.o wordhood.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/general/threadref.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c pcr.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c pcr.c pcr.c: In function 'PCR_Match_allocate': pcr.c:31:9: warning: 'g_mem_chunk_alloc' is deprecated [-Wdeprecated-declarations] pcr_match = g_chunk_new(PCR_Match, pcr->match_mem_chunk); ^~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:103, from pcr.h:23, from pcr.c:16: /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:50:17: note: declared here gpointer g_mem_chunk_alloc (GMemChunk *mem_chunk); ^~~~~~~~~~~~~~~~~ pcr.c: In function 'PCR_Probe_create': pcr.c:59:5: warning: 'g_mem_chunk_alloc' is deprecated [-Wdeprecated-declarations] register PCR_Probe *pcr_probe = g_chunk_new(PCR_Probe, ^~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:103, from pcr.h:23, from pcr.c:16: /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:50:17: note: declared here gpointer g_mem_chunk_alloc (GMemChunk *mem_chunk); ^~~~~~~~~~~~~~~~~ pcr.c: In function 'PCR_Probe_destroy': pcr.c:69:5: warning: 'g_mem_chunk_free' is deprecated [-Wdeprecated-declarations] g_mem_chunk_free(pcr->probe_mem_chunk, pcr_probe); ^~~~~~~~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:103, from pcr.h:23, from pcr.c:16: /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:54:17: note: declared here void g_mem_chunk_free (GMemChunk *mem_chunk, ^~~~~~~~~~~~~~~~ pcr.c: In function 'PCR_Sensor_create': pcr.c:155:5: warning: 'g_mem_chunk_alloc' is deprecated [-Wdeprecated-declarations] register PCR_Sensor *pcr_sensor = g_chunk_new(PCR_Sensor, ^~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:103, from pcr.h:23, from pcr.c:16: /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:50:17: note: declared here gpointer g_mem_chunk_alloc (GMemChunk *mem_chunk); ^~~~~~~~~~~~~~~~~ pcr.c: In function 'PCR_Sensor_destroy': pcr.c:174:5: warning: 'g_mem_chunk_free' is deprecated [-Wdeprecated-declarations] g_mem_chunk_free(pcr->sensor_mem_chunk, pcr_sensor); ^~~~~~~~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:103, from pcr.h:23, from pcr.c:16: /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:54:17: note: declared here void g_mem_chunk_free (GMemChunk *mem_chunk, ^~~~~~~~~~~~~~~~ pcr.c: In function 'PCR_Primer_create': pcr.c:252:5: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] g_strup(pcr_primer->forward); ^~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:79, from pcr.h:23, from pcr.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here gchar* g_strup (gchar *string); ^~~~~~~ pcr.c:253:5: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] g_strup(pcr_primer->revcomp); ^~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:79, from pcr.h:23, from pcr.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here gchar* g_strup (gchar *string); ^~~~~~~ pcr.c: In function 'PCR_create': pcr.c:357:5: warning: 'g_mem_chunk_new' is deprecated [-Wdeprecated-declarations] pcr->sensor_mem_chunk = g_mem_chunk_new("PCR_Sensor", ^~~ In file included from /usr/local/include/glib-2.0/glib.h:103, from pcr.h:23, from pcr.c:16: /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:43:17: note: declared here GMemChunk * g_mem_chunk_new (const gchar *name, ^~~~~~~~~~~~~~~ pcr.c:363:5: warning: 'g_mem_chunk_new' is deprecated [-Wdeprecated-declarations] pcr->probe_mem_chunk = g_mem_chunk_new("PCR_Probe", ^~~ In file included from /usr/local/include/glib-2.0/glib.h:103, from pcr.h:23, from pcr.c:16: /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:43:17: note: declared here GMemChunk * g_mem_chunk_new (const gchar *name, ^~~~~~~~~~~~~~~ pcr.c:366:5: warning: 'g_mem_chunk_new' is deprecated [-Wdeprecated-declarations] pcr->match_mem_chunk = g_mem_chunk_new("PCR_Match", ^~~ In file included from /usr/local/include/glib-2.0/glib.h:103, from pcr.h:23, from pcr.c:16: /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:43:17: note: declared here GMemChunk * g_mem_chunk_new (const gchar *name, ^~~~~~~~~~~~~~~ pcr.c: In function 'PCR_destroy': pcr.c:381:5: warning: 'g_mem_chunk_destroy' is deprecated [-Wdeprecated-declarations] g_mem_chunk_destroy(pcr->sensor_mem_chunk); ^~~~~~~~~~~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:103, from pcr.h:23, from pcr.c:16: /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:48:17: note: declared here void g_mem_chunk_destroy (GMemChunk *mem_chunk); ^~~~~~~~~~~~~~~~~~~ pcr.c:383:5: warning: 'g_mem_chunk_destroy' is deprecated [-Wdeprecated-declarations] g_mem_chunk_destroy(pcr->probe_mem_chunk); ^~~~~~~~~~~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:103, from pcr.h:23, from pcr.c:16: /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:48:17: note: declared here void g_mem_chunk_destroy (GMemChunk *mem_chunk); ^~~~~~~~~~~~~~~~~~~ pcr.c:384:5: warning: 'g_mem_chunk_destroy' is deprecated [-Wdeprecated-declarations] g_mem_chunk_destroy(pcr->match_mem_chunk); ^~~~~~~~~~~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:103, from pcr.h:23, from pcr.c:16: /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:48:17: note: declared here void g_mem_chunk_destroy (GMemChunk *mem_chunk); ^~~~~~~~~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o pcr.test pcr.test.o pcr.o wordhood.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/struct/fsm.o ../../src/struct/slist.o ../../src/struct/recyclebin.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c comparison.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c comparison.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o comparison.test comparison.test.o comparison.o hspset.o match.o wordhood.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/struct/recyclebin.o ../../src/struct/pqueue.o ../../src/general/threadref.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c match.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o match.test match.test.o match.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c seeder.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c seeder.c seeder.c: In function 'Seeder_decide_fsm_type': seeder.c:268:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(force_fsm, "none")) ^~ In file included from /usr/local/include/glib-2.0/glib.h:79, from seeder.h:23, from seeder.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ seeder.c:273:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(force_fsm, "normal")) ^~ In file included from /usr/local/include/glib-2.0/glib.h:79, from seeder.h:23, from seeder.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ seeder.c:275:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(force_fsm, "compact")) ^~ In file included from /usr/local/include/glib-2.0/glib.h:79, from seeder.h:23, from seeder.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o seeder.test seeder.test.o seeder.o wordhood.o hspset.o match.o comparison.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/struct/recyclebin.o ../../src/struct/fsm.o ../../src/struct/vfsm.o ../../src/struct/pqueue.o ../../src/general/threadref.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl Making all in database cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastadb.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastadb.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastadb.test fastadb.test.o fastadb.o ../../src/general/compoundfile.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastapipe.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastapipe.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastapipe.test fastapipe.test.o fastapipe.o fastadb.o ../../src/general/compoundfile.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c dataset.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c dataset.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o dataset.test dataset.test.o dataset.o fastadb.o ../../src/general/compoundfile.o ../../src/struct/bitarray.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c index.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c index.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o index.test index.test.o index.o fastadb.o dataset.o ../../src/general/compoundfile.o ../../src/general/threadref.o ../../src/struct/bitarray.o ../../src/struct/vfsm.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/struct/splaytree.o ../../src/struct/noitree.o ../../src/comparison/wordhood.o ../../src/comparison/hspset.o ../../src/comparison/match.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl Making all in c4 cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.6\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c region.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.6\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c region.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o region.test region.test.o region.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.6\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c c4.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.6\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c c4.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o c4.test c4.test.o c4.o region.o ../../src/struct/matrix.o ../../src/general/threadref.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.6\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c alignment.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.6\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c alignment.c alignment.c: In function 'AlignmentView_add_SPLICE_SITE': alignment.c:660:9: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] g_strdown(qy_seq_string); ^~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:79, from ../../src/comparison/match.h:23, from alignment.c:20: /usr/local/include/glib-2.0/glib/gstrfuncs.h:208:23: note: declared here gchar* g_strdown (gchar *string); ^~~~~~~~~ alignment.c:667:9: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] g_strdown(tg_seq_string); ^~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:79, from ../../src/comparison/match.h:23, from alignment.c:20: /usr/local/include/glib-2.0/glib/gstrfuncs.h:208:23: note: declared here gchar* g_strdown (gchar *string); ^~~~~~~~~ alignment.c:677:13: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] g_strdown(qy_seq_string); ^~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:79, from ../../src/comparison/match.h:23, from alignment.c:20: /usr/local/include/glib-2.0/glib/gstrfuncs.h:208:23: note: declared here gchar* g_strdown (gchar *string); ^~~~~~~~~ alignment.c:690:9: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] g_strdown(tg_seq_string); ^~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:79, from ../../src/comparison/match.h:23, from alignment.c:20: /usr/local/include/glib-2.0/glib/gstrfuncs.h:208:23: note: declared here gchar* g_strdown (gchar *string); ^~~~~~~~~ alignment.c: In function 'AlignmentView_add_SPLIT_CODON': alignment.c:987:5: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] g_strup(qy_codon); ^~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:79, from ../../src/comparison/match.h:23, from alignment.c:20: /usr/local/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here gchar* g_strup (gchar *string); ^~~~~~~ alignment.c:988:5: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] g_strup(tg_codon); ^~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:79, from ../../src/comparison/match.h:23, from alignment.c:20: /usr/local/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here gchar* g_strup (gchar *string); ^~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o alignment.test alignment.test.o alignment.o c4.o region.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/general/threadref.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.6\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c codegen.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.6\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c codegen.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o codegen.test codegen.test.o codegen.o ../../src/general/argument.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.6\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c optimal.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.6\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c optimal.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.6\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c layout.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.6\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c viterbi.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.6\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c subopt.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.6\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c cgutil.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o optimal.test optimal.test.o optimal.o c4.o alignment.o codegen.o region.o layout.o viterbi.o subopt.o cgutil.o ../../src/struct/slist.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/general/threadref.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.6\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c layout.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o layout.test layout.test.o layout.o ../../src/struct/matrix.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.6\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c viterbi.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o viterbi.test viterbi.test.o viterbi.o c4.o region.o alignment.o codegen.o layout.o subopt.o cgutil.o ../../src/struct/slist.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/general/threadref.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.6\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c opair.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.6\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c opair.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o opair.test opair.test.o opair.o optimal.o c4.o alignment.o codegen.o region.o layout.o viterbi.o subopt.o cgutil.o ../../src/struct/slist.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/general/threadref.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.6\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c subopt.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o subopt.test subopt.test.o subopt.o region.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.6\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c cgutil.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o cgutil.test cgutil.test.o cgutil.o codegen.o c4.o region.o ../../src/general/argument.o ../../src/struct/matrix.o ../../src/general/threadref.o -L/usr/local/lib -lglib-2.0 -lintl Making all in bsdp cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.6\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c heuristic.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.6\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c heuristic.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o heuristic.test heuristic.test.o heuristic.o ../../src/struct/slist.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/c4/c4.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/codegen.o ../../src/c4/region.o ../../src/c4/layout.o ../../src/c4/viterbi.o ../../src/c4/subopt.o ../../src/c4/cgutil.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.6\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c bsdp.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.6\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c bsdp.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o bsdp.test bsdp.test.o bsdp.o ../../src/general/argument.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.6\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c hpair.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.6\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c hpair.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.6\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c sar.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o hpair.test hpair.test.o hpair.o heuristic.o bsdp.o sar.o ../../src/struct/slist.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/comparison/hspset.o ../../src/comparison/wordhood.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/c4/c4.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/codegen.o ../../src/c4/region.o ../../src/c4/layout.o ../../src/c4/viterbi.o ../../src/c4/subopt.o ../../src/c4/cgutil.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.6\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c sar.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o sar.test sar.test.o sar.o heuristic.o ../../src/struct/slist.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/c4/c4.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/codegen.o ../../src/c4/region.o ../../src/c4/layout.o ../../src/c4/viterbi.o ../../src/c4/subopt.o ../../src/c4/cgutil.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl Making all in sdp cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.6\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c sdp.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.6\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c sdp.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.6\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c boundary.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.6\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c scheduler.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.6\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c lookahead.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.6\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c straceback.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o sdp.test sdp.test.o sdp.o boundary.o scheduler.o lookahead.o straceback.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/comparison/hspset.o ../../src/comparison/comparison.o ../../src/comparison/wordhood.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/c4/c4.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/codegen.o ../../src/c4/region.o ../../src/c4/layout.o ../../src/c4/viterbi.o ../../src/c4/subopt.o ../../src/c4/cgutil.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.6\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c lookahead.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o lookahead.test lookahead.test.o lookahead.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.6\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c boundary.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o boundary.test boundary.test.o boundary.o ../../src/general/argument.o ../../src/c4/region.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.6\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c scheduler.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o scheduler.test scheduler.test.o scheduler.o lookahead.o boundary.o straceback.o ../../src/struct/recyclebin.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/c4/c4.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/codegen.o ../../src/c4/region.o ../../src/c4/layout.o ../../src/c4/viterbi.o ../../src/c4/subopt.o ../../src/c4/cgutil.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.6\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c straceback.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o straceback.test straceback.test.o straceback.o ../../src/struct/recyclebin.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/c4/c4.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/codegen.o ../../src/c4/region.o ../../src/c4/layout.o ../../src/c4/viterbi.o ../../src/c4/subopt.o ../../src/c4/cgutil.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl Making all in model cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c edit_distance.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c edit_distance.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o edit_distance.test edit_distance.test.o edit_distance.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c affine.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c affine.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c ungapped.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o affine.test affine.test.o affine.o ungapped.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c protein2dna.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c protein2dna.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c frameshift.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o protein2dna.test protein2dna.test.o protein2dna.o affine.o ungapped.o frameshift.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c ner.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c ner.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o ner.test ner.test.o ner.o affine.o ungapped.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c est2genome.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c est2genome.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c intron.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o est2genome.test est2genome.test.o est2genome.o affine.o ungapped.o intron.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c ungapped.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o ungapped.test ungapped.test.o ungapped.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c intron.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o intron.test intron.test.o intron.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c protein2genome.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c protein2genome.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c phase.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o protein2genome.test protein2genome.test.o protein2genome.o protein2dna.o ungapped.o intron.o affine.o frameshift.o phase.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c coding2coding.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c coding2coding.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o coding2coding.test coding2coding.test.o coding2coding.o affine.o ungapped.o frameshift.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c frameshift.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o frameshift.test frameshift.test.o frameshift.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c coding2genome.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c coding2genome.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o coding2genome.test coding2genome.test.o coding2genome.o coding2coding.o affine.o ungapped.o frameshift.o intron.o phase.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c cdna2genome.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c cdna2genome.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o cdna2genome.test cdna2genome.test.o cdna2genome.o affine.o ungapped.o frameshift.o intron.o phase.o coding2coding.o coding2genome.o est2genome.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c genome2genome.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c genome2genome.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o genome2genome.test genome2genome.test.o genome2genome.o coding2coding.o affine.o ungapped.o frameshift.o intron.o phase.o coding2genome.o cdna2genome.o est2genome.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c phase.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o phase.test phase.test.o phase.o intron.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c modeltype.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c modeltype.c modeltype.c: In function 'Model_Type_from_string': modeltype.c:121:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(name[i], str)) ^~ In file included from /usr/local/include/glib-2.0/glib.h:79, from ../../src/c4/c4.h:23, from modeltype.h:23, from modeltype.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ modeltype.c:124:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(short_name[i], str)) ^~ In file included from /usr/local/include/glib-2.0/glib.h:79, from ../../src/c4/c4.h:23, from modeltype.h:23, from modeltype.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o modeltype.test modeltype.test.o modeltype.o ungapped.o affine.o est2genome.o ner.o protein2dna.o protein2genome.o coding2coding.o coding2genome.o genome2genome.o cdna2genome.o frameshift.o phase.o intron.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c bootstrapper.c bootstrapper.c: In function 'Argument_main': bootstrapper.c:421:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if((!models) || (!g_strcasecmp(models, "all"))) ^~ In file included from /usr/local/include/glib-2.0/glib.h:79, from ../../src/c4/c4.h:23, from ungapped.h:23, from bootstrapper.c:20: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o bootstrapper bootstrapper.o modeltype.o ungapped.o affine.o est2genome.o ner.o protein2dna.o protein2genome.o coding2coding.o coding2genome.o genome2genome.o cdna2genome.o frameshift.o intron.o phase.o ../../src/struct/pqueue.o ../../src/comparison/comparison.o ../../src/comparison/hspset.o ../../src/comparison/wordhood.o ../../src/bsdp/heuristic.o ../../src/sdp/sdp.o ../../src/sdp/scheduler.o ../../src/sdp/straceback.o ../../src/sdp/lookahead.o ../../src/sdp/boundary.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl Making all in hub cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/general -DHOSTTYPE="\"x86_64-portbld-dragonfly5.6\"" -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c gam.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/general -DHOSTTYPE="\"x86_64-portbld-dragonfly5.6\"" -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c gam.c gam.c: In function 'GAM_Refinement_from_string': gam.c:68:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(name[i], str)) ^~ In file included from /usr/local/include/glib-2.0/glib.h:79, from gam.h:23, from gam.c:21: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ gam.c: In function 'GAM_bestn_tree_destroy': gam.c:526:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] g_tree_traverse(bestn_tree, GAM_tree_collect_values, ^~~~~~~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:88, from gam.h:23, from gam.c:21: /usr/local/include/glib-2.0/glib/gtree.h:88:10: note: declared here void g_tree_traverse (GTree *tree, ^~~~~~~~~~~~~~~ gam.c: In function 'GAM_percent_threshold_tree_destroy': gam.c:539:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] g_tree_traverse(percent_threshold_tree, GAM_tree_collect_values, ^~~~~~~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:88, from gam.h:23, from gam.c:21: /usr/local/include/glib-2.0/glib/gtree.h:88:10: note: declared here void g_tree_traverse (GTree *tree, ^~~~~~~~~~~~~~~ gam.c: In function 'GAM_report': gam.c:589:9: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] g_tree_traverse(gam->bestn_tree, GAM_bestn_tree_report_traverse, ^~~~~~~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:88, from gam.h:23, from gam.c:21: /usr/local/include/glib-2.0/glib/gtree.h:88:10: note: declared here void g_tree_traverse (GTree *tree, ^~~~~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o gam.test gam.test.o gam.o ../../src/comparison/hspset.o ../../src/comparison/comparison.o ../../src/comparison/wordhood.o ../../src/struct/sparsecache.o ../../src/general/compoundfile.o ../../src/general/threadref.o ../../src/c4/c4.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/opair.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/region.o ../../src/c4/subopt.o ../../src/bsdp/bsdp.o ../../src/bsdp/sar.o ../../src/bsdp/heuristic.o ../../src/bsdp/hpair.o ../../src/sdp/boundary.o ../../src/sdp/sdp.o ../../src/sdp/scheduler.o ../../src/sdp/straceback.o ../../src/sdp/lookahead.o ../../src/struct/matrix.o ../../src/struct/slist.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/translate.o ../../src/sequence/splice.o ../../src/model/affine.o ../../src/model/est2genome.o ../../src/model/ner.o ../../src/model/protein2dna.o ../../src/model/protein2genome.o ../../src/model/coding2coding.o ../../src/model/coding2genome.o ../../src/model/cdna2genome.o ../../src/model/genome2genome.o ../../src/model/ungapped.o ../../src/model/intron.o ../../src/model/frameshift.o ../../src/model/phase.o ../../src/model/modeltype.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/jobqueue.o ../../src/comparison/match.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/general -DHOSTTYPE="\"x86_64-portbld-dragonfly5.6\"" -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c analysis.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/general -DHOSTTYPE="\"x86_64-portbld-dragonfly5.6\"" -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c analysis.c analysis.c: In function 'Analysis_decide_scan_query': analysis.c:329:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(force_scan, "none")){ ^~ In file included from /usr/local/include/glib-2.0/glib.h:79, from analysis.h:23, from analysis.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ analysis.c:336:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] } else if((!g_strcasecmp(force_scan, "query")) ^ In file included from /usr/local/include/glib-2.0/glib.h:79, from analysis.h:23, from analysis.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ analysis.c:337:12: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] || (!g_strcasecmp(force_scan, "q"))){ ^~ In file included from /usr/local/include/glib-2.0/glib.h:79, from analysis.h:23, from analysis.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ analysis.c:339:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] } else if((!g_strcasecmp(force_scan, "target")) ^ In file included from /usr/local/include/glib-2.0/glib.h:79, from analysis.h:23, from analysis.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ analysis.c:340:12: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] || (!g_strcasecmp(force_scan, "t"))){ ^~ In file included from /usr/local/include/glib-2.0/glib.h:79, from analysis.h:23, from analysis.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/general -DHOSTTYPE="\"x86_64-portbld-dragonfly5.6\"" -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c bsam.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o analysis.test analysis.test.o analysis.o gam.o bsam.o ../../src/comparison/hspset.o ../../src/comparison/wordhood.o ../../src/comparison/seeder.o ../../src/comparison/comparison.o ../../src/database/fastapipe.o ../../src/database/fastadb.o ../../src/struct/dejavu.o ../../src/struct/fsm.o ../../src/struct/vfsm.o ../../src/struct/sparsecache.o ../../src/general/compoundfile.o ../../src/general/socket.o ../../src/general/threadref.o ../../src/c4/c4.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/opair.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/region.o ../../src/c4/subopt.o ../../src/bsdp/bsdp.o ../../src/bsdp/sar.o ../../src/bsdp/heuristic.o ../../src/bsdp/hpair.o ../../src/sdp/boundary.o ../../src/sdp/sdp.o ../../src/sdp/scheduler.o ../../src/sdp/straceback.o ../../src/sdp/lookahead.o ../../src/struct/matrix.o ../../src/struct/slist.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/translate.o ../../src/sequence/splice.o ../../src/model/affine.o ../../src/model/est2genome.o ../../src/model/ner.o ../../src/model/protein2dna.o ../../src/model/protein2genome.o ../../src/model/coding2coding.o ../../src/model/coding2genome.o ../../src/model/cdna2genome.o ../../src/model/genome2genome.o ../../src/model/ungapped.o ../../src/model/intron.o ../../src/model/frameshift.o ../../src/model/phase.o ../../src/model/modeltype.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/jobqueue.o ../../src/comparison/match.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/general -DHOSTTYPE="\"x86_64-portbld-dragonfly5.6\"" -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c bsam.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o bsam.test bsam.test.o bsam.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o ../../src/comparison/hspset.o ../../src/comparison/comparison.o ../../src/comparison/match.o ../../src/comparison/wordhood.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/translate.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/sequence/splice.o ../../src/struct/dejavu.o ../../src/struct/pqueue.o ../../src/struct/sparsecache.o ../../src/struct/recyclebin.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl Making all in program cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/hub -I../../src/general -DHOSTTYPE="\"x86_64-portbld-dragonfly5.6\"" -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: 16:52:57.515: Starting building bootstrapping components ** Message: 16:52:57.515: Processing model [u] ** Message: 16:52:57.516: Bootstrapper processing model [ungapped:dna2dna] ** Message: 16:52:57.516: Process optimal [optimal:ungapped:dna2dna] ** (process:491962): WARNING **: 16:52:57.516: Creating codegen directory [/construction/biology/exonerate/exonerate-2.4.0/codegen] ** (process:491962): WARNING **: 16:52:57.516: Creating codegen directory [/construction/biology/exonerate/exonerate-2.4.0/codegen] ** (process:491962): WARNING **: 16:52:57.516: Creating codegen directory [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6] ** (process:491962): WARNING **: 16:52:57.516: Creating codegen directory [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6] ** Message: 16:52:57.516: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_dna2dna_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_dna2dna_32_find_32_score.c ** Message: 16:52:57.656: 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_dragonfly5_46_6/optimal_58_ungapped_58_dna2dna_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_dna2dna_32_find_32_path.c ** Message: 16:52:57.824: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_dna2dna_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_dna2dna_32_find_32_region.c ** Message: 16:52:58.204: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.c ** Message: 16:52:58.459: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 16:52:58.716: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_dna2dna_32_find_32_score.o] ** Message: 16:52:58.717: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_dna2dna_32_find_32_score.o] to archive ar -cSq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_dna2dna_32_find_32_score.o ** Message: 16:52:58.720: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_score] ** Message: 16:52:58.720: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_dna2dna_32_find_32_path.o] ** Message: 16:52:58.720: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_dna2dna_32_find_32_path.o ** Message: 16:52:58.724: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_path] ** Message: 16:52:58.724: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_dna2dna_32_find_32_region.o] ** Message: 16:52:58.724: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_dna2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_dna2dna_32_find_32_region.o ** Message: 16:52:58.727: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_region] ** Message: 16:52:58.727: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.o] ** Message: 16:52:58.727: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.o ** Message: 16:52:58.731: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint] ** Message: 16:52:58.731: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 16:52:58.731: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 16:52:58.734: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation] ** Message: 16:52:58.734: Bootstrapper processing model [ungapped:protein2protein] ** Message: 16:52:58.734: Process optimal [optimal:ungapped:protein2protein] ** Message: 16:52:58.734: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_protein2protein_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_protein2protein_32_find_32_score.c ** Message: 16:52:58.876: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_protein2protein_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_protein2protein_32_find_32_path.c ** Message: 16:52:59.035: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_protein2protein_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_protein2protein_32_find_32_region.c ** Message: 16:52:59.210: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.c ** Message: 16:52:59.476: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.c ** Message: 16:52:59.878: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_protein2protein_32_find_32_score.o] ** Message: 16:52:59.878: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_protein2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_protein2protein_32_find_32_score.o ** Message: 16:52:59.882: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_score] ** Message: 16:52:59.882: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_protein2protein_32_find_32_path.o] ** Message: 16:52:59.882: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_protein2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_protein2protein_32_find_32_path.o ** Message: 16:52:59.886: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_path] ** Message: 16:52:59.886: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_protein2protein_32_find_32_region.o] ** Message: 16:52:59.886: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_protein2protein_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_protein2protein_32_find_32_region.o ** Message: 16:52:59.889: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_region] ** Message: 16:52:59.890: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.o] ** Message: 16:52:59.890: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.o ** Message: 16:52:59.893: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint] ** Message: 16:52:59.893: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.o] ** Message: 16:52:59.893: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.o ** Message: 16:52:59.897: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation] ** Message: 16:52:59.897: Bootstrapper processing model [ungapped:dna2protein] ** Message: 16:52:59.897: Process optimal [optimal:ungapped:dna2protein] ** Message: 16:52:59.897: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_dna2protein_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_dna2protein_32_find_32_score.c ** Message: 16:53:00.118: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_dna2protein_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_dna2protein_32_find_32_path.c ** Message: 16:53:00.349: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_dna2protein_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_dna2protein_32_find_32_region.c ** Message: 16:53:00.723: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.c ** Message: 16:53:01.039: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.c ** Message: 16:53:01.359: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_dna2protein_32_find_32_score.o] ** Message: 16:53:01.359: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_dna2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_dna2protein_32_find_32_score.o ** Message: 16:53:01.363: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_score] ** Message: 16:53:01.363: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_dna2protein_32_find_32_path.o] ** Message: 16:53:01.363: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_dna2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_dna2protein_32_find_32_path.o ** Message: 16:53:01.367: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_path] ** Message: 16:53:01.367: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_dna2protein_32_find_32_region.o] ** Message: 16:53:01.367: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_dna2protein_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_dna2protein_32_find_32_region.o ** Message: 16:53:01.370: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_region] ** Message: 16:53:01.371: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.o] ** Message: 16:53:01.371: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.o ** Message: 16:53:01.374: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint] ** Message: 16:53:01.374: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.o] ** Message: 16:53:01.374: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.o ** Message: 16:53:01.378: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation] ** Message: 16:53:01.378: Bootstrapper processing model [ungapped:protein2dna] ** Message: 16:53:01.378: Process optimal [optimal:ungapped:protein2dna] ** Message: 16:53:01.378: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_protein2dna_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_protein2dna_32_find_32_score.c ** Message: 16:53:01.557: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_protein2dna_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_protein2dna_32_find_32_path.c ** Message: 16:53:01.770: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_protein2dna_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_protein2dna_32_find_32_region.c ** Message: 16:53:02.066: 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_dragonfly5_46_6/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.c ** Message: 16:53:02.772: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.c ** Message: 16:53:03.203: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_protein2dna_32_find_32_score.o] ** Message: 16:53:03.203: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_protein2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_protein2dna_32_find_32_score.o ** Message: 16:53:03.208: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_score] ** Message: 16:53:03.208: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_protein2dna_32_find_32_path.o] ** Message: 16:53:03.208: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_protein2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_protein2dna_32_find_32_path.o ** Message: 16:53:03.212: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_path] ** Message: 16:53:03.212: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_protein2dna_32_find_32_region.o] ** Message: 16:53:03.212: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_protein2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_protein2dna_32_find_32_region.o ** Message: 16:53:03.216: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_region] ** Message: 16:53:03.216: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.o] ** Message: 16:53:03.216: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.o ** Message: 16:53:03.220: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint] ** Message: 16:53:03.220: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.o] ** Message: 16:53:03.220: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.o ** Message: 16:53:03.224: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation] ** Message: 16:53:03.224: Processing model [u:t] ** Message: 16:53:03.224: Bootstrapper processing model [ungapped:codon] ** Message: 16:53:03.224: Process optimal [optimal:ungapped:codon] ** Message: 16:53:03.225: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_codon_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_codon_32_find_32_score.c ** Message: 16:53:03.686: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_codon_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_codon_32_find_32_path.c ** Message: 16:53:04.065: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_codon_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_codon_32_find_32_region.c ** Message: 16:53:04.516: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_codon_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_codon_32_find_32_checkpoint.c ** Message: 16:53:05.158: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.c ** Message: 16:53:06.022: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_codon_32_find_32_score.o] ** Message: 16:53:06.022: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_codon_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_codon_32_find_32_score.o ** Message: 16:53:06.027: Adding function [optimal_58_ungapped_58_codon_32_find_32_score] ** Message: 16:53:06.027: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_codon_32_find_32_path.o] ** Message: 16:53:06.027: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_codon_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_codon_32_find_32_path.o ** Message: 16:53:06.031: Adding function [optimal_58_ungapped_58_codon_32_find_32_path] ** Message: 16:53:06.031: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_codon_32_find_32_region.o] ** Message: 16:53:06.031: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_codon_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_codon_32_find_32_region.o ** Message: 16:53:06.035: Adding function [optimal_58_ungapped_58_codon_32_find_32_region] ** Message: 16:53:06.045: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_codon_32_find_32_checkpoint.o] ** Message: 16:53:06.045: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_codon_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_codon_32_find_32_checkpoint.o ** Message: 16:53:06.049: Adding function [optimal_58_ungapped_58_codon_32_find_32_checkpoint] ** Message: 16:53:06.049: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.o] ** Message: 16:53:06.049: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.o ** Message: 16:53:06.053: Adding function [optimal_58_ungapped_58_codon_32_find_32_path_32_continuation] ** Message: 16:53:06.054: Processing model [a:g] ** Message: 16:53:06.054: Bootstrapper processing model [affine:global:dna2dna] ** Message: 16:53:06.054: Process optimal [optimal:affine:global:dna2dna] ** Message: 16:53:06.055: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.c ** Message: 16:53:06.600: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.c ** Message: 16:53:07.820: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.c ** Message: 16:53:09.061: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 16:53:10.282: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.o] ** Message: 16:53:10.282: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.o ** Message: 16:53:10.286: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_score] ** Message: 16:53:10.286: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.o] ** Message: 16:53:10.286: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.o ** Message: 16:53:10.291: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_path] ** Message: 16:53:10.292: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.o] ** Message: 16:53:10.292: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.o ** Message: 16:53:10.296: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint] ** Message: 16:53:10.296: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 16:53:10.296: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 16:53:10.300: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation] ** Message: 16:53:10.300: Bootstrapper processing model [affine:global:protein2protein] ** Message: 16:53:10.301: Process optimal [optimal:affine:global:protein2protein] ** Message: 16:53:10.301: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.c ** Message: 16:53:10.955: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.c ** Message: 16:53:12.040: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.c ** Message: 16:53:12.956: 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_dragonfly5_46_6/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.c ** Message: 16:53:14.185: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.o] ** Message: 16:53:14.185: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.o ** Message: 16:53:14.189: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_score] ** Message: 16:53:14.189: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.o] ** Message: 16:53:14.189: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.o ** Message: 16:53:14.193: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_path] ** Message: 16:53:14.193: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.o] ** Message: 16:53:14.193: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.o ** Message: 16:53:14.198: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint] ** Message: 16:53:14.198: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.o] ** Message: 16:53:14.198: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.o ** Message: 16:53:14.203: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation] ** Message: 16:53:14.203: Processing model [a:b] ** Message: 16:53:14.204: Bootstrapper processing model [affine:bestfit:dna2dna] ** Message: 16:53:14.204: Process optimal [optimal:affine:bestfit:dna2dna] ** Message: 16:53:14.205: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.c ** Message: 16:53:15.098: 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_dragonfly5_46_6/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.c ** Message: 16:53:17.225: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.c ** Message: 16:53:18.302: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.c ** Message: 16:53:19.019: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 16:53:20.085: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.o] ** Message: 16:53:20.085: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.o ** Message: 16:53:20.092: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score] ** Message: 16:53:20.092: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.o] ** Message: 16:53:20.092: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.o ** Message: 16:53:20.096: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path] ** Message: 16:53:20.096: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.o] ** Message: 16:53:20.096: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.o ** Message: 16:53:20.105: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region] ** Message: 16:53:20.105: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.o] ** Message: 16:53:20.105: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.o ** Message: 16:53:20.109: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint] ** Message: 16:53:20.109: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 16:53:20.109: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 16:53:20.114: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation] ** Message: 16:53:20.115: Bootstrapper processing model [affine:bestfit:protein2protein] ** Message: 16:53:20.115: Process optimal [optimal:affine:bestfit:protein2protein] ** Message: 16:53:20.116: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.c ** Message: 16:53:21.015: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.c ** Message: 16:53:22.933: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.c ** Message: 16:53:24.046: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.c ** Message: 16:53:24.669: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.c ** Message: 16:53:25.670: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.o] ** Message: 16:53:25.671: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.o ** Message: 16:53:25.685: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score] ** Message: 16:53:25.686: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.o] ** Message: 16:53:25.686: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.o ** Message: 16:53:25.690: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path] ** Message: 16:53:25.690: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.o] ** Message: 16:53:25.690: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.o ** Message: 16:53:25.705: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region] ** Message: 16:53:25.705: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.o] ** Message: 16:53:25.705: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.o ** Message: 16:53:25.710: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint] ** Message: 16:53:25.710: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.o] ** Message: 16:53:25.710: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.o ** Message: 16:53:25.716: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation] ** Message: 16:53:25.716: Processing model [a:l] ** Message: 16:53:25.716: Bootstrapper processing model [affine:local:dna2dna] ** Message: 16:53:25.716: Process optimal [optimal:affine:local:dna2dna] ** Message: 16:53:25.716: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.c ** Message: 16:53:25.957: 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_dragonfly5_46_6/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.c ** Message: 16:53:26.276: 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_dragonfly5_46_6/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.c ** Message: 16:53:26.597: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.c ** Message: 16:53:27.369: 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_dragonfly5_46_6/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 16:53:28.261: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.o] ** Message: 16:53:28.261: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.o ** Message: 16:53:28.265: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_score] ** Message: 16:53:28.266: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.o] ** Message: 16:53:28.266: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.o ** Message: 16:53:28.270: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_path] ** Message: 16:53:28.270: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.o] ** Message: 16:53:28.270: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.o ** Message: 16:53:28.275: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_region] ** Message: 16:53:28.275: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o] ** Message: 16:53:28.275: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o ** Message: 16:53:28.279: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint] ** Message: 16:53:28.279: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 16:53:28.279: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 16:53:28.285: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation] ** Message: 16:53:28.287: Process optimal [Terminal [Segment("START"->"match"):[affine:local:dna2dna]]] ** Message: 16:53:28.288: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:53:28.991: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:53:29.919: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:53:29.919: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:53:29.924: 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: 16:53:29.924: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:53:29.924: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:53:29.929: 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: 16:53:29.929: Process optimal [Terminal [Segment("match"->"END"):[affine:local:dna2dna]]] ** Message: 16:53:29.930: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:53:30.408: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:53:31.205: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:53:31.205: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:53:31.209: 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: 16:53:31.209: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:53:31.209: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:53:31.214: 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: 16:53:31.214: Process optimal [HeuristicJoin:[Segment("match"->"match"):[affine:local:dna2dna]]] ** Message: 16:53:31.216: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:53:33.133: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:53:36.734: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:53:36.734: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:53:36.739: 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: 16:53:36.739: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:53:36.739: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:53:36.743: 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: 16:53:36.744: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.c ** Message: 16:53:36.958: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.c ** Message: 16:53:37.215: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.o] ** Message: 16:53:37.215: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.o ** Message: 16:53:37.221: Adding function [Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded] ** Message: 16:53:37.221: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.o] ** Message: 16:53:37.221: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.o ** Message: 16:53:37.226: Adding function [Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded] ** Message: 16:53:37.227: Bootstrapper processing model [affine:local:protein2protein] ** Message: 16:53:37.227: Process optimal [optimal:affine:local:protein2protein] ** Message: 16:53:37.227: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.c ** Message: 16:53:37.447: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.c ** Message: 16:53:37.788: 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_dragonfly5_46_6/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.c ** Message: 16:53:38.159: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.c ** Message: 16:53:39.360: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.c ** Message: 16:53:40.720: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.o] ** Message: 16:53:40.720: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.o ** Message: 16:53:40.725: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_score] ** Message: 16:53:40.726: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.o] ** Message: 16:53:40.726: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.o ** Message: 16:53:40.731: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_path] ** Message: 16:53:40.731: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.o] ** Message: 16:53:40.731: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.o ** Message: 16:53:40.736: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_region] ** Message: 16:53:40.736: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o] ** Message: 16:53:40.736: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o ** Message: 16:53:40.742: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint] ** Message: 16:53:40.743: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o] ** Message: 16:53:40.743: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o ** Message: 16:53:40.748: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation] ** Message: 16:53:40.750: Process optimal [Terminal [Segment("START"->"match"):[affine:local:protein2protein]]] ** Message: 16:53:40.751: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:53:41.498: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:53:43.610: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:53:43.611: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:53:43.616: 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: 16:53:43.616: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:53:43.616: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:53:43.623: 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: 16:53:43.623: Process optimal [Terminal [Segment("match"->"END"):[affine:local:protein2protein]]] ** Message: 16:53:43.624: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:53:44.076: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:53:44.870: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:53:44.871: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:53:44.886: 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: 16:53:44.886: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:53:44.886: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:53:44.892: 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: 16:53:44.892: Process optimal [HeuristicJoin:[Segment("match"->"match"):[affine:local:protein2protein]]] ** Message: 16:53:44.893: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:53:46.897: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:53:53.810: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:53:53.810: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:53:53.815: 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: 16:53:53.816: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:53:53.816: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:53:53.821: 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: 16:53:53.822: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.c ** Message: 16:53:54.056: 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_dragonfly5_46_6/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.c ** Message: 16:53:54.354: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.o] ** Message: 16:53:54.354: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.o ** Message: 16:53:54.359: Adding function [Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded] ** Message: 16:53:54.359: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.o] ** Message: 16:53:54.359: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.o ** Message: 16:53:54.364: Adding function [Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded] ** Message: 16:53:54.364: Processing model [a:o] ** Message: 16:53:54.364: Bootstrapper processing model [affine:overlap:dna2dna] ** Message: 16:53:54.364: Process optimal [optimal:affine:overlap:dna2dna] ** Message: 16:53:54.365: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.c ** Message: 16:53:54.853: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.c ** Message: 16:53:56.388: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.c ** Message: 16:53:58.740: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.c ** Message: 16:53:59.903: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 16:54:01.330: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.o] ** Message: 16:54:01.330: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.o ** Message: 16:54:01.336: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score] ** Message: 16:54:01.336: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.o] ** Message: 16:54:01.336: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.o ** Message: 16:54:01.341: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path] ** Message: 16:54:01.341: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.o] ** Message: 16:54:01.341: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.o ** Message: 16:54:01.348: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region] ** Message: 16:54:01.348: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.o] ** Message: 16:54:01.348: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.o ** Message: 16:54:01.353: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint] ** Message: 16:54:01.354: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 16:54:01.354: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 16:54:01.359: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation] ** Message: 16:54:01.360: Processing model [e2g] ** Message: 16:54:01.360: Bootstrapper processing model [est2genome] ** Message: 16:54:01.360: Process optimal [optimal:est2genome] ** Message: 16:54:01.362: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_est2genome_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_est2genome_32_find_32_score.c ** Message: 16:54:03.100: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_est2genome_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_est2genome_32_find_32_path.c ** Message: 16:54:05.708: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_est2genome_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_est2genome_32_find_32_region.c ** Message: 16:54:07.436: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_est2genome_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_est2genome_32_find_32_checkpoint.c ** Message: 16:54:12.396: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_est2genome_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_est2genome_32_find_32_path_32_continuation.c ** Message: 16:54:20.698: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_est2genome_32_find_32_score.o] ** Message: 16:54:20.698: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_est2genome_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_est2genome_32_find_32_score.o ** Message: 16:54:20.704: Adding function [optimal_58_est2genome_32_find_32_score] ** Message: 16:54:20.704: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_est2genome_32_find_32_path.o] ** Message: 16:54:20.704: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_est2genome_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_est2genome_32_find_32_path.o ** Message: 16:54:20.710: Adding function [optimal_58_est2genome_32_find_32_path] ** Message: 16:54:20.710: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_est2genome_32_find_32_region.o] ** Message: 16:54:20.710: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_est2genome_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_est2genome_32_find_32_region.o ** Message: 16:54:20.717: Adding function [optimal_58_est2genome_32_find_32_region] ** Message: 16:54:20.717: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_est2genome_32_find_32_checkpoint.o] ** Message: 16:54:20.717: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_est2genome_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_est2genome_32_find_32_checkpoint.o ** Message: 16:54:20.722: Adding function [optimal_58_est2genome_32_find_32_checkpoint] ** Message: 16:54:20.722: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_est2genome_32_find_32_path_32_continuation.o] ** Message: 16:54:20.722: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_est2genome_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_est2genome_32_find_32_path_32_continuation.o ** Message: 16:54:20.728: Adding function [optimal_58_est2genome_32_find_32_path_32_continuation] ** Message: 16:54:20.736: Process optimal [Terminal [Segment("START"->"match reverse"):[est2genome]]] ** Message: 16:54:20.738: 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_dragonfly5_46_6/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:54:22.832: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:54:27.115: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:54:27.116: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:54:27.122: 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: 16:54:27.122: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:54:27.122: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:54:27.128: 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: 16:54:27.128: Process optimal [Terminal [Segment("match reverse"->"END"):[est2genome]]] ** Message: 16:54:27.130: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:54:28.504: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:54:30.039: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:54:30.040: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:54:30.045: 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: 16:54:30.045: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:54:30.045: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:54:30.052: 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: 16:54:30.052: Process optimal [Terminal [Segment("START"->"match forward"):[est2genome]]] ** Message: 16:54:30.053: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:54:32.430: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:54:41.199: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:54:41.199: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:54:41.206: 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: 16:54:41.206: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:54:41.206: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:54:41.212: 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: 16:54:41.212: Process optimal [Terminal [Segment("match forward"->"END"):[est2genome]]] ** Message: 16:54:41.214: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:54:42.621: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:54:44.337: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:54:44.337: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:54:44.343: 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: 16:54:44.343: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:54:44.343: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:54:44.349: 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: 16:54:44.349: Process optimal [HeuristicJoin:[Segment("match reverse"->"match reverse"):[est2genome]]] ** Message: 16:54:44.353: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:54:53.143: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:55:02.831: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:55:02.831: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:55:02.837: 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: 16:55:02.837: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:55:02.837: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:55:02.843: 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: 16:55:02.843: Process optimal [Src span [Segment("match reverse"->"intron reverse"):[est2genome]]] ** Message: 16:55:02.844: 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_dragonfly5_46_6/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:55:03.561: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:55:05.537: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:55:05.537: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:55:05.544: 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: 16:55:05.544: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:55:05.544: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:55:05.551: 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: 16:55:05.551: Process optimal [Src span traceback [Segment("match reverse"->"intron reverse"):[est2genome]]] ** Message: 16:55:05.555: 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_dragonfly5_46_6/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:55:12.139: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:55:12.139: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:55:12.146: 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: 16:55:12.146: Process optimal [Dst span [Segment("intron reverse"->"match reverse"):[est2genome]]] ** Message: 16:55:12.148: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:55:15.273: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:55:18.379: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:55:18.379: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:55:18.386: 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: 16:55:18.386: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:55:18.386: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:55:18.392: 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: 16:55:18.393: Process optimal [HeuristicJoin:[Segment("match forward"->"match forward"):[est2genome]]] ** Message: 16:55:18.396: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:55:22.196: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:55:28.743: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:55:28.744: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:55:28.751: 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: 16:55:28.751: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:55:28.751: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:55:28.761: 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: 16:55:28.761: Process optimal [Src span [Segment("match forward"->"intron forward"):[est2genome]]] ** Message: 16:55:28.764: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:55:29.969: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:55:32.402: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:55:32.402: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:55:32.409: 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: 16:55:32.409: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:55:32.409: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:55:32.417: 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: 16:55:32.417: Process optimal [Src span traceback [Segment("match forward"->"intron forward"):[est2genome]]] ** Message: 16:55:32.421: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:55:41.520: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:55:41.520: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:55:41.527: 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: 16:55:41.527: Process optimal [Dst span [Segment("intron forward"->"match forward"):[est2genome]]] ** Message: 16:55:41.530: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:55:44.497: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:55:55.437: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:55:55.437: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:55:55.466: 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: 16:55:55.466: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:55:55.466: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:55:55.472: 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: 16:55:55.473: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.c ** Message: 16:55:56.408: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.c ** Message: 16:55:57.489: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.o] ** Message: 16:55:57.489: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.o ** Message: 16:55:57.496: Adding function [Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary] ** Message: 16:55:57.496: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.o] ** Message: 16:55:57.496: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.o ** Message: 16:55:57.503: Adding function [Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary] ** Message: 16:55:57.504: Processing model [ner] ** Message: 16:55:57.504: Bootstrapper processing model [NER:affine:local:dna2dna] ** Message: 16:55:57.504: Process optimal [optimal:NER:affine:local:dna2dna] ** Message: 16:55:57.505: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.c ** Message: 16:55:58.044: 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_dragonfly5_46_6/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.c ** Message: 16:55:58.731: 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_dragonfly5_46_6/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.c ** Message: 16:55:59.619: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.c ** Message: 16:56:01.388: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 16:56:03.609: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.o] ** Message: 16:56:03.609: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.o ** Message: 16:56:03.617: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score] ** Message: 16:56:03.617: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.o] ** Message: 16:56:03.617: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.o ** Message: 16:56:03.624: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path] ** Message: 16:56:03.624: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.o] ** Message: 16:56:03.625: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.o ** Message: 16:56:03.632: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region] ** Message: 16:56:03.632: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o] ** Message: 16:56:03.632: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o ** Message: 16:56:03.650: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint] ** Message: 16:56:03.650: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 16:56:03.650: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 16:56:03.669: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation] ** Message: 16:56:03.673: Process optimal [Terminal [Segment("START"->"match"):[NER:affine:local:dna2dna]]] ** Message: 16:56:03.675: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:04.789: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:07.918: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:07.919: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:07.926: 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: 16:56:07.926: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:07.926: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:07.933: 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: 16:56:07.933: Process optimal [Terminal [Segment("match"->"END"):[NER:affine:local:dna2dna]]] ** Message: 16:56:07.934: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:08.699: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:09.838: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:09.838: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:09.845: 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: 16:56:09.846: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:09.846: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:09.852: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path] ** Message: 16:56:09.852: Process optimal [HeuristicJoin:[Segment("match"->"match"):[NER:affine:local:dna2dna]]] ** Message: 16:56:09.865: 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_dragonfly5_46_6/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:12.738: 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_dragonfly5_46_6/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:21.190: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:21.191: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:21.198: 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: 16:56:21.198: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:21.198: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:21.205: 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: 16:56:21.205: Process optimal [Src span [Segment("match"->"ner"):[NER:affine:local:dna2dna]]] ** Message: 16:56:21.207: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:22.446: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:24.336: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:24.336: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:24.344: 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: 16:56:24.344: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:24.344: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:24.351: 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: 16:56:24.351: Process optimal [Src span traceback [Segment("match"->"ner"):[NER:affine:local:dna2dna]]] ** Message: 16:56:24.354: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:29.971: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:29.971: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:29.978: 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: 16:56:29.978: Process optimal [Dst span [Segment("ner"->"match"):[NER:affine:local:dna2dna]]] ** Message: 16:56:29.980: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:31.673: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:34.096: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:34.096: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:34.103: 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: 16:56:34.103: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:34.103: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:34.121: 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: 16:56:34.121: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.c ** Message: 16:56:34.486: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.c ** Message: 16:56:35.100: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.o] ** Message: 16:56:35.100: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.o ** Message: 16:56:35.109: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary] ** Message: 16:56:35.109: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.o] ** Message: 16:56:35.109: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.o ** Message: 16:56:35.128: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary] ** Message: 16:56:35.128: Bootstrapper processing model [NER:affine:local:protein2protein] ** Message: 16:56:35.128: Process optimal [optimal:NER:affine:local:protein2protein] ** Message: 16:56:35.129: 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_dragonfly5_46_6/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.c ** Message: 16:56:35.361: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.c ** Message: 16:56:35.800: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.c ** Message: 16:56:36.258: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.c ** Message: 16:56:37.499: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.c ** Message: 16:56:38.694: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.o] ** Message: 16:56:38.694: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.o ** Message: 16:56:38.712: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score] ** Message: 16:56:38.712: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.o] ** Message: 16:56:38.712: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.o ** Message: 16:56:38.721: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path] ** Message: 16:56:38.721: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.o] ** Message: 16:56:38.721: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.o ** Message: 16:56:38.730: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region] ** Message: 16:56:38.730: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o] ** Message: 16:56:38.730: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o ** Message: 16:56:38.739: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint] ** Message: 16:56:38.739: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o] ** Message: 16:56:38.739: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o ** Message: 16:56:38.747: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation] ** Message: 16:56:38.751: Process optimal [Terminal [Segment("START"->"match"):[NER:affine:local:protein2protein]]] ** Message: 16:56:38.753: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:40.044: 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_dragonfly5_46_6/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:41.986: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:41.987: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:41.994: 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: 16:56:41.994: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:41.994: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:42.003: 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: 16:56:42.003: Process optimal [Terminal [Segment("match"->"END"):[NER:affine:local:protein2protein]]] ** Message: 16:56:42.004: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:42.520: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:43.530: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:43.530: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:43.547: 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: 16:56:43.547: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:43.547: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:43.565: 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: 16:56:43.565: Process optimal [HeuristicJoin:[Segment("match"->"match"):[NER:affine:local:protein2protein]]] ** Message: 16:56:43.568: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:45.559: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:51.860: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:51.860: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:51.877: 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: 16:56:51.877: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:51.878: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:51.894: 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: 16:56:51.895: Process optimal [Src span [Segment("match"->"ner"):[NER:affine:local:protein2protein]]] ** Message: 16:56:51.896: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:53.177: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:54.348: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:54.348: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:54.357: 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: 16:56:54.357: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:54.357: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:54.365: 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: 16:56:54.365: Process optimal [Src span traceback [Segment("match"->"ner"):[NER:affine:local:protein2protein]]] ** Message: 16:56:54.368: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:57.755: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:57.755: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:57.764: 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: 16:56:57.764: Process optimal [Dst span [Segment("ner"->"match"):[NER:affine:local:protein2protein]]] ** Message: 16:56:57.765: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:56:58.832: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:57:00.816: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:57:00.816: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:57:00.825: 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: 16:57:00.825: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:57:00.826: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:57:00.834: 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: 16:57:00.835: 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_dragonfly5_46_6/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.c ** Message: 16:57:01.157: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.c ** Message: 16:57:01.697: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.o] ** Message: 16:57:01.697: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.o ** Message: 16:57:01.715: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary] ** Message: 16:57:01.716: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.o] ** Message: 16:57:01.716: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.o ** Message: 16:57:01.724: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary] ** Message: 16:57:01.724: Processing model [p2d] ** Message: 16:57:01.725: Bootstrapper processing model [protein2dna:local] ** Message: 16:57:01.725: Process optimal [optimal:protein2dna:local] ** Message: 16:57:01.726: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2dna_58_local_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2dna_58_local_32_find_32_score.c ** Message: 16:57:02.489: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2dna_58_local_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2dna_58_local_32_find_32_path.c ** Message: 16:57:03.323: 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_dragonfly5_46_6/optimal_58_protein2dna_58_local_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2dna_58_local_32_find_32_region.c ** Message: 16:57:04.391: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2dna_58_local_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2dna_58_local_32_find_32_checkpoint.c ** Message: 16:57:06.559: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.c ** Message: 16:57:09.221: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2dna_58_local_32_find_32_score.o] ** Message: 16:57:09.222: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2dna_58_local_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2dna_58_local_32_find_32_score.o ** Message: 16:57:09.230: Adding function [optimal_58_protein2dna_58_local_32_find_32_score] ** Message: 16:57:09.230: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2dna_58_local_32_find_32_path.o] ** Message: 16:57:09.231: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2dna_58_local_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2dna_58_local_32_find_32_path.o ** Message: 16:57:09.239: Adding function [optimal_58_protein2dna_58_local_32_find_32_path] ** Message: 16:57:09.239: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2dna_58_local_32_find_32_region.o] ** Message: 16:57:09.239: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2dna_58_local_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2dna_58_local_32_find_32_region.o ** Message: 16:57:09.257: Adding function [optimal_58_protein2dna_58_local_32_find_32_region] ** Message: 16:57:09.257: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2dna_58_local_32_find_32_checkpoint.o] ** Message: 16:57:09.257: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2dna_58_local_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2dna_58_local_32_find_32_checkpoint.o ** Message: 16:57:09.276: Adding function [optimal_58_protein2dna_58_local_32_find_32_checkpoint] ** Message: 16:57:09.276: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.o] ** Message: 16:57:09.276: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.o ** Message: 16:57:09.284: Adding function [optimal_58_protein2dna_58_local_32_find_32_path_32_continuation] ** Message: 16:57:09.291: Process optimal [Terminal [Segment("START"->"match"):[protein2dna:local]]] ** Message: 16:57:09.293: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:57:11.351: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:57:15.511: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:57:15.511: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:57:15.518: 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: 16:57:15.518: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:57:15.518: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:57:15.528: 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: 16:57:15.528: Process optimal [Terminal [Segment("match"->"END"):[protein2dna:local]]] ** Message: 16:57:15.529: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:57:16.522: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:57:17.795: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:57:17.795: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:57:17.802: 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: 16:57:17.802: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:57:17.802: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:57:17.811: 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: 16:57:17.811: Process optimal [HeuristicJoin:[Segment("match"->"match"):[protein2dna:local]]] ** Message: 16:57:17.815: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:57:23.582: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:57:32.500: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:57:32.500: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:57:32.509: 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: 16:57:32.509: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:57:32.509: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:57:32.519: 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: 16:57:32.520: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.c ** Message: 16:57:32.801: 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_dragonfly5_46_6/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.c ** Message: 16:57:33.346: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.o] ** Message: 16:57:33.346: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.o ** Message: 16:57:33.356: Adding function [Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded] ** Message: 16:57:33.356: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.o] ** Message: 16:57:33.356: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.o ** Message: 16:57:33.365: Adding function [Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded] ** Message: 16:57:33.365: Processing model [p2d:b] ** Message: 16:57:33.366: Bootstrapper processing model [protein2dna:bestfit] ** Message: 16:57:33.366: Process optimal [optimal:protein2dna:bestfit] ** Message: 16:57:33.369: 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_dragonfly5_46_6/optimal_58_protein2dna_58_bestfit_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2dna_58_bestfit_32_find_32_score.c ** Message: 16:57:36.651: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2dna_58_bestfit_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2dna_58_bestfit_32_find_32_path.c ** Message: 16:57:41.581: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2dna_58_bestfit_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2dna_58_bestfit_32_find_32_region.c ** Message: 16:57:46.933: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.c ** Message: 16:57:49.466: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.c ** Message: 16:57:53.772: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2dna_58_bestfit_32_find_32_score.o] ** Message: 16:57:53.772: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2dna_58_bestfit_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2dna_58_bestfit_32_find_32_score.o ** Message: 16:57:53.782: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_score] ** Message: 16:57:53.782: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2dna_58_bestfit_32_find_32_path.o] ** Message: 16:57:53.782: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2dna_58_bestfit_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2dna_58_bestfit_32_find_32_path.o ** Message: 16:57:53.791: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_path] ** Message: 16:57:53.792: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2dna_58_bestfit_32_find_32_region.o] ** Message: 16:57:53.792: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2dna_58_bestfit_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2dna_58_bestfit_32_find_32_region.o ** Message: 16:57:53.802: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_region] ** Message: 16:57:53.802: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.o] ** Message: 16:57:53.802: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.o ** Message: 16:57:53.811: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint] ** Message: 16:57:53.811: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.o] ** Message: 16:57:53.811: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.o ** Message: 16:57:53.821: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation] ** Message: 16:57:53.821: Processing model [p2g] ** Message: 16:57:53.822: Bootstrapper processing model [protein2genome:local] ** Message: 16:57:53.822: Process optimal [optimal:protein2genome:local] ** Message: 16:57:53.824: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2genome_58_local_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2genome_58_local_32_find_32_score.c ** Message: 16:57:55.945: 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_dragonfly5_46_6/optimal_58_protein2genome_58_local_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2genome_58_local_32_find_32_path.c ** Message: 16:58:01.754: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2genome_58_local_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2genome_58_local_32_find_32_region.c ** Message: 16:58:03.986: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2genome_58_local_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2genome_58_local_32_find_32_checkpoint.c ** Message: 16:58:10.249: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.c ** Message: 16:58:22.576: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2genome_58_local_32_find_32_score.o] ** Message: 16:58:22.576: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2genome_58_local_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2genome_58_local_32_find_32_score.o ** Message: 16:58:22.586: Adding function [optimal_58_protein2genome_58_local_32_find_32_score] ** Message: 16:58:22.586: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2genome_58_local_32_find_32_path.o] ** Message: 16:58:22.586: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2genome_58_local_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2genome_58_local_32_find_32_path.o ** Message: 16:58:22.596: Adding function [optimal_58_protein2genome_58_local_32_find_32_path] ** Message: 16:58:22.596: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2genome_58_local_32_find_32_region.o] ** Message: 16:58:22.596: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2genome_58_local_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2genome_58_local_32_find_32_region.o ** Message: 16:58:22.607: Adding function [optimal_58_protein2genome_58_local_32_find_32_region] ** Message: 16:58:22.607: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2genome_58_local_32_find_32_checkpoint.o] ** Message: 16:58:22.607: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2genome_58_local_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2genome_58_local_32_find_32_checkpoint.o ** Message: 16:58:22.617: Adding function [optimal_58_protein2genome_58_local_32_find_32_checkpoint] ** Message: 16:58:22.617: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.o] ** Message: 16:58:22.617: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.o ** Message: 16:58:22.627: Adding function [optimal_58_protein2genome_58_local_32_find_32_path_32_continuation] ** Message: 16:58:22.656: Process optimal [Terminal [Segment("START"->"match"):[protein2genome:local]]] ** Message: 16:58:22.661: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:58:30.439: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:58:54.950: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:58:54.950: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:58:54.961: 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: 16:58:54.961: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:58:54.961: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:58:54.971: 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: 16:58:54.971: Process optimal [Terminal [Segment("match"->"END"):[protein2genome:local]]] ** Message: 16:58:55.020: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:59:01.987: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:59:12.903: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:59:12.904: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:59:12.913: 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: 16:59:12.913: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:59:12.913: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:59:12.924: 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: 16:59:12.924: Process optimal [HeuristicJoin:[Segment("match"->"match"):[protein2genome:local]]] ** Message: 16:59:12.933: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 16:59:42.245: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:00:18.811: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:00:18.811: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:00:18.821: 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: 17:00:18.821: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:00:18.821: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:00:18.831: 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: 17:00:18.831: Process optimal [Src span [Segment("match"->"intron 0:0 phase-T"):[protein2genome:local]]] ** Message: 17:00:18.834: 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_dragonfly5_46_6/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:00:23.713: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:00:32.028: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:00:32.028: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:00:32.039: 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: 17:00:32.039: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:00:32.039: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:00:32.050: 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: 17:00:32.050: Process optimal [Src span traceback [Segment("match"->"intron 0:0 phase-T"):[protein2genome:local]]] ** Message: 17:00:32.060: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:01:06.341: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:01:06.341: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:01:06.353: 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: 17:01:06.353: Process optimal [Dst span [Segment("intron 0:0 phase-T"->"match"):[protein2genome:local]]] ** Message: 17:01:06.359: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:01:14.626: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:01:28.912: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:01:28.912: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:01:28.922: 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: 17:01:28.922: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:01:28.922: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:01:28.933: 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: 17:01:28.933: Process optimal [Src span [Segment("match"->"intron 1:2 phase-T"):[protein2genome:local]]] ** Message: 17:01:28.936: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:01:32.314: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:01:37.595: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:01:37.595: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:01:37.607: 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: 17:01:37.607: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:01:37.607: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:01:37.619: 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: 17:01:37.619: Process optimal [Src span traceback [Segment("match"->"intron 1:2 phase-T"):[protein2genome:local]]] ** Message: 17:01:37.628: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:02:13.326: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:02:13.327: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:02:13.339: 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: 17:02:13.339: Process optimal [Dst span [Segment("intron 1:2 phase-T"->"match"):[protein2genome:local]]] ** Message: 17:02:13.344: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:02:25.638: 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_dragonfly5_46_6/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:02:44.435: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:02:44.435: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:02:44.446: 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: 17:02:44.446: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:02:44.446: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:02:44.457: 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: 17:02:44.457: Process optimal [Src span [Segment("match"->"intron 2:1 phase-T"):[protein2genome:local]]] ** Message: 17:02:44.460: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:02:48.841: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:02:55.807: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:02:55.807: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:02:55.819: 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: 17:02:55.819: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:02:55.819: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:02:55.830: 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: 17:02:55.830: Process optimal [Src span traceback [Segment("match"->"intron 2:1 phase-T"):[protein2genome:local]]] ** Message: 17:02:55.839: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:03:29.054: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:03:29.054: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:03:29.066: 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: 17:03:29.066: Process optimal [Dst span [Segment("intron 2:1 phase-T"->"match"):[protein2genome:local]]] ** Message: 17:03:29.072: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:03:41.060: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:04:03.251: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:04:03.251: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:04:03.263: 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: 17:04:03.263: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:04:03.263: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:04:03.275: 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: 17:04:03.276: 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_dragonfly5_46_6/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.c ** Message: 17:04:03.746: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.c ** Message: 17:04:04.371: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.o] ** Message: 17:04:04.371: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.o ** Message: 17:04:04.383: Adding function [Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary] ** Message: 17:04:04.383: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.o] ** Message: 17:04:04.383: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.o ** Message: 17:04:04.396: Adding function [Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary] ** Message: 17:04:04.396: Processing model [p2g:b] ** Message: 17:04:04.397: Bootstrapper processing model [protein2genome:bestfit] ** Message: 17:04:04.397: Process optimal [optimal:protein2genome:bestfit] ** Message: 17:04:04.404: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2genome_58_bestfit_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2genome_58_bestfit_32_find_32_score.c ** Message: 17:04:15.371: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2genome_58_bestfit_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2genome_58_bestfit_32_find_32_path.c ** Message: 17:04:31.008: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2genome_58_bestfit_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2genome_58_bestfit_32_find_32_region.c ** Message: 17:04:40.283: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.c ** Message: 17:04:47.262: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.c ** Message: 17:05:00.694: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2genome_58_bestfit_32_find_32_score.o] ** Message: 17:05:00.694: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2genome_58_bestfit_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2genome_58_bestfit_32_find_32_score.o ** Message: 17:05:00.707: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_score] ** Message: 17:05:00.707: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2genome_58_bestfit_32_find_32_path.o] ** Message: 17:05:00.707: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2genome_58_bestfit_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2genome_58_bestfit_32_find_32_path.o ** Message: 17:05:00.720: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_path] ** Message: 17:05:00.721: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2genome_58_bestfit_32_find_32_region.o] ** Message: 17:05:00.721: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2genome_58_bestfit_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2genome_58_bestfit_32_find_32_region.o ** Message: 17:05:00.733: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_region] ** Message: 17:05:00.733: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.o] ** Message: 17:05:00.733: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.o ** Message: 17:05:00.746: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint] ** Message: 17:05:00.746: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.o] ** Message: 17:05:00.746: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.o ** Message: 17:05:00.759: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation] ** Message: 17:05:00.759: Processing model [c2c] ** Message: 17:05:00.760: Bootstrapper processing model [coding2coding] ** Message: 17:05:00.760: Process optimal [optimal:coding2coding] ** Message: 17:05:00.762: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_coding2coding_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_coding2coding_32_find_32_score.c ** Message: 17:05:03.099: 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_dragonfly5_46_6/optimal_58_coding2coding_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_coding2coding_32_find_32_path.c ** Message: 17:05:08.186: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_coding2coding_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_coding2coding_32_find_32_region.c ** Message: 17:05:13.691: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_coding2coding_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_coding2coding_32_find_32_checkpoint.c ** Message: 17:05:32.332: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_coding2coding_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_coding2coding_32_find_32_path_32_continuation.c ** Message: 17:05:58.396: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_coding2coding_32_find_32_score.o] ** Message: 17:05:58.396: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_coding2coding_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_coding2coding_32_find_32_score.o ** Message: 17:05:58.409: Adding function [optimal_58_coding2coding_32_find_32_score] ** Message: 17:05:58.409: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_coding2coding_32_find_32_path.o] ** Message: 17:05:58.409: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_coding2coding_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_coding2coding_32_find_32_path.o ** Message: 17:05:58.424: Adding function [optimal_58_coding2coding_32_find_32_path] ** Message: 17:05:58.424: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_coding2coding_32_find_32_region.o] ** Message: 17:05:58.424: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_coding2coding_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_coding2coding_32_find_32_region.o ** Message: 17:05:58.437: Adding function [optimal_58_coding2coding_32_find_32_region] ** Message: 17:05:58.438: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_coding2coding_32_find_32_checkpoint.o] ** Message: 17:05:58.438: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_coding2coding_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_coding2coding_32_find_32_checkpoint.o ** Message: 17:05:58.451: Adding function [optimal_58_coding2coding_32_find_32_checkpoint] ** Message: 17:05:58.451: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_coding2coding_32_find_32_path_32_continuation.o] ** Message: 17:05:58.451: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_coding2coding_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_coding2coding_32_find_32_path_32_continuation.o ** Message: 17:05:58.463: Adding function [optimal_58_coding2coding_32_find_32_path_32_continuation] ** Message: 17:05:58.508: Process optimal [Terminal [Segment("START"->"match"):[coding2coding]]] ** Message: 17:05:58.514: 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_dragonfly5_46_6/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:06:15.616: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:06:51.547: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:06:51.547: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:06:51.560: 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: 17:06:51.560: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:06:51.560: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:06:51.573: 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: 17:06:51.574: Process optimal [Terminal [Segment("match"->"END"):[coding2coding]]] ** Message: 17:06:51.576: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:06:57.350: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:07:05.055: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:07:05.055: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:07:05.069: 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: 17:07:05.069: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:07:05.070: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:07:05.084: 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: 17:07:05.084: Process optimal [HeuristicJoin:[Segment("match"->"match"):[coding2coding]]] ** Message: 17:07:05.092: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:07:40.809: 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_dragonfly5_46_6/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:08:53.001: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:08:53.001: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:08:53.014: 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: 17:08:53.015: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:08:53.015: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/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: 17:08:53.029: 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: 17:08:53.030: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.c ** Message: 17:08:53.612: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.c ** Message: 17:08:54.080: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.o] ** Message: 17:08:54.081: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.o ** Message: 17:08:54.095: Adding function [Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded] ** Message: 17:08:54.095: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.o] ** Message: 17:08:54.095: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.o ** Message: 17:08:54.109: Adding function [Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded] ** Message: 17:08:54.110: Processing model [c2g] ** Message: 17:08:54.111: Bootstrapper processing model [coding2genome] ** Message: 17:08:54.111: Process optimal [optimal:coding2genome] ** Message: 17:08:54.115: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_coding2genome_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_coding2genome_32_find_32_score.c ** Message: 17:09:00.009: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_coding2genome_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_coding2genome_32_find_32_path.c ** Message: 17:09:09.626: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_coding2genome_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_coding2genome_32_find_32_region.c ** Message: 17:09:18.139: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_coding2genome_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_coding2genome_32_find_32_checkpoint.c ** Message: 17:09:55.904: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_coding2genome_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_coding2genome_32_find_32_path_32_continuation.c ** Message: 17:11:04.099: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_coding2genome_32_find_32_score.o] ** Message: 17:11:04.099: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_coding2genome_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_coding2genome_32_find_32_score.o ** Message: 17:11:04.113: Adding function [optimal_58_coding2genome_32_find_32_score] ** Message: 17:11:04.114: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_coding2genome_32_find_32_path.o] ** Message: 17:11:04.114: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_coding2genome_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_coding2genome_32_find_32_path.o ** Message: 17:11:04.128: Adding function [optimal_58_coding2genome_32_find_32_path] ** Message: 17:11:04.128: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_coding2genome_32_find_32_region.o] ** Message: 17:11:04.128: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_coding2genome_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_coding2genome_32_find_32_region.o ** Message: 17:11:04.142: Adding function [optimal_58_coding2genome_32_find_32_region] ** Message: 17:11:04.143: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_coding2genome_32_find_32_checkpoint.o] ** Message: 17:11:04.143: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_coding2genome_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_coding2genome_32_find_32_checkpoint.o ** Message: 17:11:04.157: Adding function [optimal_58_coding2genome_32_find_32_checkpoint] ** Message: 17:11:04.157: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_coding2genome_32_find_32_path_32_continuation.o] ** Message: 17:11:04.157: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_coding2genome_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_coding2genome_32_find_32_path_32_continuation.o ** Message: 17:11:04.171: Adding function [optimal_58_coding2genome_32_find_32_path_32_continuation] ** Message: 17:11:04.172: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.c ** Message: 17:11:05.035: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.c ** Message: 17:11:06.354: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.o] ** Message: 17:11:06.354: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.o ** Message: 17:11:06.369: Adding function [Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary] ** Message: 17:11:06.369: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.o] ** Message: 17:11:06.369: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.o ** Message: 17:11:06.395: Adding function [Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary] ** Message: 17:11:06.395: Processing model [cd2g] ** Message: 17:11:06.397: Bootstrapper processing model [cdna2genome] ** Message: 17:11:06.397: Process optimal [optimal:cdna2genome] ** Message: 17:11:06.406: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_cdna2genome_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_cdna2genome_32_find_32_score.c ** Message: 17:11:40.087: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_cdna2genome_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_cdna2genome_32_find_32_path.c ** Message: 17:12:38.529: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_cdna2genome_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_cdna2genome_32_find_32_region.c ** Message: 17:13:16.000: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_cdna2genome_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_cdna2genome_32_find_32_checkpoint.c ** Message: 17:16:43.941: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_cdna2genome_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_cdna2genome_32_find_32_path_32_continuation.c ** Message: 17:22:48.482: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_cdna2genome_32_find_32_score.o] ** Message: 17:22:48.482: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_cdna2genome_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_cdna2genome_32_find_32_score.o ** Message: 17:22:48.496: Adding function [optimal_58_cdna2genome_32_find_32_score] ** Message: 17:22:48.496: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_cdna2genome_32_find_32_path.o] ** Message: 17:22:48.496: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_cdna2genome_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_cdna2genome_32_find_32_path.o ** Message: 17:22:48.511: Adding function [optimal_58_cdna2genome_32_find_32_path] ** Message: 17:22:48.511: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_cdna2genome_32_find_32_region.o] ** Message: 17:22:48.511: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_cdna2genome_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_cdna2genome_32_find_32_region.o ** Message: 17:22:48.527: Adding function [optimal_58_cdna2genome_32_find_32_region] ** Message: 17:22:48.527: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_cdna2genome_32_find_32_checkpoint.o] ** Message: 17:22:48.527: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_cdna2genome_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_cdna2genome_32_find_32_checkpoint.o ** Message: 17:22:48.542: Adding function [optimal_58_cdna2genome_32_find_32_checkpoint] ** Message: 17:22:48.542: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_cdna2genome_32_find_32_path_32_continuation.o] ** Message: 17:22:48.542: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_cdna2genome_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/optimal_58_cdna2genome_32_find_32_path_32_continuation.o ** Message: 17:22:48.558: Adding function [optimal_58_cdna2genome_32_find_32_path_32_continuation] ** Message: 17:22:48.559: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.c ** Message: 17:22:49.946: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.c ** Message: 17:22:52.200: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o] ** Message: 17:22:52.200: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o ** Message: 17:22:52.216: Adding function [Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary] ** Message: 17:22:52.217: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o] ** Message: 17:22:52.217: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_6/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o ** Message: 17:22:52.233: Adding function [Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary] ** Message: 17:22:52.233: 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: 17:22:52.503: Adding: [c4_model_lookup.o] ** Message: 17:22:52.503: Adding object file [c4_model_lookup.o] to archive ar -Sq c4_model_archive.a c4_model_lookup.o ** Message: 17:22:52.521: Indexing archive [c4_model_archive.a] ranlib c4_model_archive.a ** Message: 17:22:52.562: Done ** Message: 17:22:52.563: Finished building bootstrapping components cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/hub -I../../src/general -DHOSTTYPE="\"x86_64-portbld-dragonfly5.6\"" -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I. -DUSE_COMPILED_MODELS -c ../../src/c4/viterbi.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/hub -I../../src/general -DHOSTTYPE="\"x86_64-portbld-dragonfly5.6\"" -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I. -DUSE_COMPILED_MODELS -c ../../src/sdp/scheduler.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o exonerate exonerate.o viterbi.o scheduler.o c4_model_archive.a ../../src/comparison/wordhood.o ../../src/comparison/hspset.o ../../src/comparison/seeder.o ../../src/comparison/comparison.o ../../src/database/fastapipe.o ../../src/database/fastadb.o ../../src/struct/dejavu.o ../../src/struct/fsm.o ../../src/struct/vfsm.o ../../src/struct/sparsecache.o ../../src/hub/gam.o ../../src/hub/bsam.o ../../src/hub/analysis.o ../../src/general/compoundfile.o ../../src/general/threadref.o ../../src/c4/c4.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/opair.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/layout.o ../../src/c4/region.o ../../src/c4/subopt.o ../../src/bsdp/bsdp.o ../../src/bsdp/sar.o ../../src/bsdp/heuristic.o ../../src/bsdp/hpair.o ../../src/sdp/boundary.o ../../src/sdp/sdp.o ../../src/sdp/lookahead.o ../../src/sdp/straceback.o ../../src/struct/matrix.o ../../src/struct/slist.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/translate.o ../../src/sequence/splice.o ../../src/model/affine.o ../../src/model/est2genome.o ../../src/model/ner.o ../../src/model/protein2dna.o ../../src/model/protein2genome.o ../../src/model/coding2coding.o ../../src/model/coding2genome.o ../../src/model/cdna2genome.o ../../src/model/genome2genome.o ../../src/model/ungapped.o ../../src/model/intron.o ../../src/model/frameshift.o ../../src/model/phase.o ../../src/model/modeltype.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/socket.o ../../src/general/jobqueue.o ../../src/comparison/match.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/hub -I../../src/general -DHOSTTYPE="\"x86_64-portbld-dragonfly5.6\"" -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c ipcress.c ipcress.c: In function 'Ipcress_prepare_PCR': ipcress.c:264:9: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] g_strup(primer_a); ^~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:79, from ipcress.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here gchar* g_strup (gchar *string); ^~~~~~~ ipcress.c:265:9: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] g_strup(primer_b); ^~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:79, from ipcress.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here gchar* g_strup (gchar *string); ^~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o ipcress ipcress.o ../../src/comparison/pcr.o ../../src/comparison/wordhood.o ../../src/database/fastadb.o ../../src/sequence/alphabet.o ../../src/sequence/sequence.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/struct/fsm.o ../../src/struct/slist.o ../../src/struct/matrix.o ../../src/struct/recyclebin.o ../../src/struct/sparsecache.o ../../src/general/lineparse.o ../../src/general/argument.o ../../src/general/compoundfile.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/hub -I../../src/general -DHOSTTYPE="\"x86_64-portbld-dragonfly5.6\"" -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c exonerate-server.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o exonerate-server exonerate-server.o ../../src/general/socket.o ../../src/general/argument.o ../../src/comparison/hspset.o ../../src/comparison/match.o ../../src/comparison/wordhood.o ../../src/database/dataset.o ../../src/database/index.o ../../src/database/fastadb.o ../../src/struct/bitarray.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/struct/splaytree.o ../../src/struct/noitree.o ../../src/struct/vfsm.o ../../src/struct/pqueue.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/translate.o ../../src/sequence/splice.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl Making all in util cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastaclean.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastaclean fastaclean.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastaclip.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastaclip fastaclip.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastachecksum.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastachecksum fastachecksum.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastacomposition.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastacomposition fastacomposition.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastadiff.c fastadiff.c: In function 'fasta_diff': fastadiff.c:70:13: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] comp = g_strcasecmp; ^~~~ In file included from /usr/local/include/glib-2.0/glib.h:79, from ../../src/general/argument.h:26, from fastadiff.c:19: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastadiff fastadiff.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastaexplode.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastaexplode fastaexplode.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastafetch.c fastafetch.c: In function 'get_query_list': fastafetch.c:121:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(query, "stdin")){ ^~ In file included from /usr/local/include/glib-2.0/glib.h:79, from ../../src/general/argument.h:26, from fastafetch.c:21: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastafetch fastafetch.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastahardmask.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastahardmask fastahardmask.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastaindex.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastaindex fastaindex.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastalength.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastalength fastalength.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastanrdb.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastanrdb fastanrdb.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastaoverlap.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastaoverlap fastaoverlap.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastareformat.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastareformat fastareformat.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastaremove.c fastaremove.c: In function 'Argument_main': fastaremove.c:73:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(remove_path, "stdin")){ ^~ In file included from /usr/local/include/glib-2.0/glib.h:79, from ../../src/general/argument.h:26, from fastaremove.c:19: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastaremove fastaremove.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastarevcomp.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastarevcomp fastarevcomp.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastasoftmask.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastasoftmask fastasoftmask.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastasort.c fastasort.c: In function 'SortKey_Mask_create': fastasort.c:130:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(sort_key, "id")) ^~ In file included from /usr/local/include/glib-2.0/glib.h:79, from ../../src/general/argument.h:26, from fastasort.c:20: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ fastasort.c:132:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] else if(!g_strcasecmp(sort_key, "len")) ^~~~ In file included from /usr/local/include/glib-2.0/glib.h:79, from ../../src/general/argument.h:26, from fastasort.c:20: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ fastasort.c:134:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] else if(!g_strcasecmp(sort_key, "seq")) ^~~~ In file included from /usr/local/include/glib-2.0/glib.h:79, from ../../src/general/argument.h:26, from fastasort.c:20: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastasort fastasort.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastasplit.c fastasplit.c: In function 'Argument_main': fastasplit.c:92:13: warning: 'g_basename' is deprecated: Use 'g_path_get_basename' instead [-Wdeprecated-declarations] output_dir, G_DIR_SEPARATOR, g_basename(query_path)); ^~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:48, from ../../src/general/argument.h:26, from fastasplit.c:20: /usr/local/include/glib-2.0/glib/gfileutils.h:163:14: note: declared here const gchar *g_basename (const gchar *file_name); ^~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastasplit fastasplit.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastasubseq.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastasubseq fastasubseq.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastatranslate.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastatranslate fastatranslate.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastavalidcds.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastavalidcds fastavalidcds.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fasta2esd.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fasta2esd fasta2esd.o ../../src/database/dataset.o ../../src/struct/bitarray.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastaannotatecdna.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastaannotatecdna fastaannotatecdna.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c esd2esi.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o esd2esi esd2esi.o ../../src/database/dataset.o ../../src/database/index.o ../../src/general/threadref.o ../../src/struct/bitarray.o ../../src/struct/vfsm.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/struct/noitree.o ../../src/struct/splaytree.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/comparison/wordhood.o ../../src/comparison/hspset.o ../../src/comparison/match.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl Making all in test Making all in data Making all in cdna Making all in protein Making all in exonerate Making all in ipcress Making all in util -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- 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) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for exonerate-2.4.0 file sizes/checksums [34]: . done packing files [34]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Wednesday, 24 JUL 2019 at 17:23:15 UTC Duration: 00:31:24