=> Building biology/exonerate Started : Thursday, 7 MAR 2019 at 18:13:53 UTC Platform: 5.5-DEVELOPMENT DragonFly v5.5.0.192.g15ae7f0-DEVELOPMENT #34: Tue Feb 19 09:07:07 PST 2019 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.5-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.5-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=5.5 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-BE 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=5.26.2 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=8 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500500 OSVERSION=9999999 OSREL=5.5 _OSRELEASE=5.5-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-1.10.5_5.txz Installing pkg-1.10.5_5... Extracting pkg-1.10.5_5: .......... 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-1.6.0,1.txz Installing pkgconf-1.6.0,1... Extracting pkgconf-1.6.0,1: .......... 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_3,1.txz Installing glib-2.56.3_3,1... `-- Installing gettext-runtime-0.19.8.1_2... | `-- Installing indexinfo-0.3.1... | `-- Extracting indexinfo-0.3.1: .... done `-- Extracting gettext-runtime-0.19.8.1_2: .......... 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 libxml2-2.9.8... `-- Extracting libxml2-2.9.8: .......... done `-- Installing pcre-8.42_1... `-- Extracting pcre-8.42_1: .......... done `-- Installing python27-2.7.15... | `-- Installing expat-2.2.6_1... | `-- Extracting expat-2.2.6_1: .......... done | `-- Installing libressl-2.8.3... | `-- Extracting libressl-2.8.3: .......... done | `-- Installing ncurses-6.1.20190112... | `-- Extracting ncurses-6.1.20190112: .......... done | `-- Installing readline-7.0.5... | `-- Extracting readline-7.0.5: .......... done `-- Extracting python27-2.7.15: .......... done Extracting glib-2.56.3_3,1: .......... done No schema files found: doing nothing. Message from python27-2.7.15: =========================================================================== Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: bsddb databases/py-bsddb gdbm databases/py-gdbm sqlite3 databases/py-sqlite3 tkinter x11-toolkits/py-tkinter =========================================================================== ===> 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-dragonfly5.5 checking host system type... x86_64-portbld-dragonfly5.5 Set host to x86_64-portbld-dragonfly5.5 x86_64-portbld-dragonfly5.5 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-dragonfly5.5\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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-dragonfly5.5\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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-dragonfly5.5\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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-dragonfly5.5\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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-dragonfly5.5\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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-dragonfly5.5\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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-dragonfly5.5\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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-dragonfly5.5\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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-dragonfly5.5\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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-dragonfly5.5\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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-dragonfly5.5\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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-dragonfly5.5\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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-dragonfly5.5\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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-dragonfly5.5\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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-dragonfly5.5\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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-dragonfly5.5\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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-dragonfly5.5\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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-dragonfly5.5\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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-dragonfly5.5\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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-dragonfly5.5\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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-dragonfly5.5\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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-dragonfly5.5\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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-dragonfly5.5\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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-dragonfly5.5\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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-dragonfly5.5\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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-dragonfly5.5\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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-dragonfly5.5\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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-dragonfly5.5\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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-dragonfly5.5\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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-dragonfly5.5\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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-dragonfly5.5\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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-dragonfly5.5\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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-dragonfly5.5\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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-dragonfly5.5\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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-dragonfly5.5\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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-dragonfly5.5\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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-dragonfly5.5\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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-dragonfly5.5\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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-dragonfly5.5\"" -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-dragonfly5.5\"" -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-dragonfly5.5\"" -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-dragonfly5.5\"" -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-dragonfly5.5\"" -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-dragonfly5.5\"" -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-dragonfly5.5\"" -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: 18:15:02.451: Starting building bootstrapping components ** Message: 18:15:02.451: Processing model [u] ** Message: 18:15:02.452: Bootstrapper processing model [ungapped:dna2dna] ** Message: 18:15:02.452: Process optimal [optimal:ungapped:dna2dna] ** (process:592486): WARNING **: 18:15:02.452: Creating codegen directory [/construction/biology/exonerate/exonerate-2.4.0/codegen] ** (process:592486): WARNING **: 18:15:02.452: Creating codegen directory [/construction/biology/exonerate/exonerate-2.4.0/codegen] ** (process:592486): WARNING **: 18:15:02.452: Creating codegen directory [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5] ** (process:592486): WARNING **: 18:15:02.452: Creating codegen directory [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5] ** Message: 18:15:02.452: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_ungapped_58_dna2dna_32_find_32_score.c ** Message: 18:15:02.712: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_ungapped_58_dna2dna_32_find_32_path.c ** Message: 18:15:03.405: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_ungapped_58_dna2dna_32_find_32_region.c ** Message: 18:15:03.711: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.c ** Message: 18:15:04.231: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 18:15:04.926: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_ungapped_58_dna2dna_32_find_32_score.o] ** Message: 18:15:04.926: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_ungapped_58_dna2dna_32_find_32_score.o ** Message: 18:15:04.933: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_score] ** Message: 18:15:04.933: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_ungapped_58_dna2dna_32_find_32_path.o] ** Message: 18:15:04.933: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_ungapped_58_dna2dna_32_find_32_path.o ** Message: 18:15:04.938: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_path] ** Message: 18:15:04.938: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_ungapped_58_dna2dna_32_find_32_region.o] ** Message: 18:15:04.938: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_ungapped_58_dna2dna_32_find_32_region.o ** Message: 18:15:04.942: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_region] ** Message: 18:15:04.943: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.o] ** Message: 18:15:04.943: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.o ** Message: 18:15:04.948: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint] ** Message: 18:15:04.948: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 18:15:04.948: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 18:15:04.953: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation] ** Message: 18:15:04.953: Bootstrapper processing model [ungapped:protein2protein] ** Message: 18:15:04.953: Process optimal [optimal:ungapped:protein2protein] ** Message: 18:15:04.953: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_ungapped_58_protein2protein_32_find_32_score.c ** Message: 18:15:05.131: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_ungapped_58_protein2protein_32_find_32_path.c ** Message: 18:15:05.601: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_ungapped_58_protein2protein_32_find_32_region.c ** Message: 18:15:05.986: 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_5/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_5/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.c ** Message: 18:15:06.327: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.c ** Message: 18:15:07.324: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_ungapped_58_protein2protein_32_find_32_score.o] ** Message: 18:15:07.324: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_ungapped_58_protein2protein_32_find_32_score.o ** Message: 18:15:07.328: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_score] ** Message: 18:15:07.328: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_ungapped_58_protein2protein_32_find_32_path.o] ** Message: 18:15:07.328: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_ungapped_58_protein2protein_32_find_32_path.o ** Message: 18:15:07.333: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_path] ** Message: 18:15:07.333: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_ungapped_58_protein2protein_32_find_32_region.o] ** Message: 18:15:07.333: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_ungapped_58_protein2protein_32_find_32_region.o ** Message: 18:15:07.338: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_region] ** Message: 18:15:07.338: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.o] ** Message: 18:15:07.338: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.o ** Message: 18:15:07.343: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint] ** Message: 18:15:07.343: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.o] ** Message: 18:15:07.343: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.o ** Message: 18:15:07.348: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation] ** Message: 18:15:07.348: Bootstrapper processing model [ungapped:dna2protein] ** Message: 18:15:07.348: Process optimal [optimal:ungapped:dna2protein] ** Message: 18:15:07.348: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_ungapped_58_dna2protein_32_find_32_score.c ** Message: 18:15:07.982: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_ungapped_58_dna2protein_32_find_32_path.c ** Message: 18:15:08.430: 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_5/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_5/optimal_58_ungapped_58_dna2protein_32_find_32_region.c ** Message: 18:15:08.986: 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_5/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_5/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.c ** Message: 18:15:09.825: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.c ** Message: 18:15:10.784: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_ungapped_58_dna2protein_32_find_32_score.o] ** Message: 18:15:10.784: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_ungapped_58_dna2protein_32_find_32_score.o ** Message: 18:15:10.789: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_score] ** Message: 18:15:10.789: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_ungapped_58_dna2protein_32_find_32_path.o] ** Message: 18:15:10.789: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_ungapped_58_dna2protein_32_find_32_path.o ** Message: 18:15:10.793: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_path] ** Message: 18:15:10.794: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_ungapped_58_dna2protein_32_find_32_region.o] ** Message: 18:15:10.794: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_ungapped_58_dna2protein_32_find_32_region.o ** Message: 18:15:10.800: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_region] ** Message: 18:15:10.800: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.o] ** Message: 18:15:10.800: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.o ** Message: 18:15:10.805: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint] ** Message: 18:15:10.805: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.o] ** Message: 18:15:10.806: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.o ** Message: 18:15:10.811: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation] ** Message: 18:15:10.812: Bootstrapper processing model [ungapped:protein2dna] ** Message: 18:15:10.812: Process optimal [optimal:ungapped:protein2dna] ** Message: 18:15:10.812: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_ungapped_58_protein2dna_32_find_32_score.c ** Message: 18:15:11.663: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_ungapped_58_protein2dna_32_find_32_path.c ** Message: 18:15:12.088: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_ungapped_58_protein2dna_32_find_32_region.c ** Message: 18:15:12.344: 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_5/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_5/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.c ** Message: 18:15:13.223: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.c ** Message: 18:15:13.884: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_ungapped_58_protein2dna_32_find_32_score.o] ** Message: 18:15:13.884: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_ungapped_58_protein2dna_32_find_32_score.o ** Message: 18:15:13.892: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_score] ** Message: 18:15:13.892: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_ungapped_58_protein2dna_32_find_32_path.o] ** Message: 18:15:13.892: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_ungapped_58_protein2dna_32_find_32_path.o ** Message: 18:15:13.900: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_path] ** Message: 18:15:13.900: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_ungapped_58_protein2dna_32_find_32_region.o] ** Message: 18:15:13.900: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_ungapped_58_protein2dna_32_find_32_region.o ** Message: 18:15:13.908: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_region] ** Message: 18:15:13.908: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.o] ** Message: 18:15:13.908: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.o ** Message: 18:15:13.916: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint] ** Message: 18:15:13.916: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.o] ** Message: 18:15:13.916: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.o ** Message: 18:15:13.934: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation] ** Message: 18:15:13.934: Processing model [u:t] ** Message: 18:15:13.934: Bootstrapper processing model [ungapped:codon] ** Message: 18:15:13.934: Process optimal [optimal:ungapped:codon] ** Message: 18:15:13.935: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_ungapped_58_codon_32_find_32_score.c ** Message: 18:15:14.493: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_ungapped_58_codon_32_find_32_path.c ** Message: 18:15:15.167: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_ungapped_58_codon_32_find_32_region.c ** Message: 18:15:15.957: 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_5/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_5/optimal_58_ungapped_58_codon_32_find_32_checkpoint.c ** Message: 18:15:17.591: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.c ** Message: 18:15:18.609: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_ungapped_58_codon_32_find_32_score.o] ** Message: 18:15:18.609: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_ungapped_58_codon_32_find_32_score.o ** Message: 18:15:18.615: Adding function [optimal_58_ungapped_58_codon_32_find_32_score] ** Message: 18:15:18.615: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_ungapped_58_codon_32_find_32_path.o] ** Message: 18:15:18.615: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_ungapped_58_codon_32_find_32_path.o ** Message: 18:15:18.621: Adding function [optimal_58_ungapped_58_codon_32_find_32_path] ** Message: 18:15:18.621: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_ungapped_58_codon_32_find_32_region.o] ** Message: 18:15:18.621: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_ungapped_58_codon_32_find_32_region.o ** Message: 18:15:18.627: Adding function [optimal_58_ungapped_58_codon_32_find_32_region] ** Message: 18:15:18.627: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_ungapped_58_codon_32_find_32_checkpoint.o] ** Message: 18:15:18.627: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_ungapped_58_codon_32_find_32_checkpoint.o ** Message: 18:15:18.631: Adding function [optimal_58_ungapped_58_codon_32_find_32_checkpoint] ** Message: 18:15:18.632: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.o] ** Message: 18:15:18.632: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.o ** Message: 18:15:18.637: Adding function [optimal_58_ungapped_58_codon_32_find_32_path_32_continuation] ** Message: 18:15:18.637: Processing model [a:g] ** Message: 18:15:18.637: Bootstrapper processing model [affine:global:dna2dna] ** Message: 18:15:18.637: Process optimal [optimal:affine:global:dna2dna] ** Message: 18:15:18.638: 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_5/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_5/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.c ** Message: 18:15:20.086: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.c ** Message: 18:15:20.628: 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_5/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_5/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.c ** Message: 18:15:22.016: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 18:15:24.269: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.o] ** Message: 18:15:24.269: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.o ** Message: 18:15:24.275: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_score] ** Message: 18:15:24.275: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.o] ** Message: 18:15:24.275: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.o ** Message: 18:15:24.281: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_path] ** Message: 18:15:24.281: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.o] ** Message: 18:15:24.281: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.o ** Message: 18:15:24.287: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint] ** Message: 18:15:24.287: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 18:15:24.287: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 18:15:24.294: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation] ** Message: 18:15:24.295: Bootstrapper processing model [affine:global:protein2protein] ** Message: 18:15:24.295: Process optimal [optimal:affine:global:protein2protein] ** Message: 18:15:24.296: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.c ** Message: 18:15:24.708: 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_5/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_5/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.c ** Message: 18:15:25.322: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.c ** Message: 18:15:25.936: 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_5/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_5/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.c ** Message: 18:15:26.961: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.o] ** Message: 18:15:26.962: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.o ** Message: 18:15:26.967: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_score] ** Message: 18:15:26.967: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.o] ** Message: 18:15:26.967: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.o ** Message: 18:15:26.973: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_path] ** Message: 18:15:26.973: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.o] ** Message: 18:15:26.973: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.o ** Message: 18:15:26.979: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint] ** Message: 18:15:26.979: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.o] ** Message: 18:15:26.979: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.o ** Message: 18:15:26.984: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation] ** Message: 18:15:26.985: Processing model [a:b] ** Message: 18:15:26.985: Bootstrapper processing model [affine:bestfit:dna2dna] ** Message: 18:15:26.985: Process optimal [optimal:affine:bestfit:dna2dna] ** Message: 18:15:26.986: 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_5/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_5/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.c ** Message: 18:15:28.323: 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_5/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_5/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.c ** Message: 18:15:29.799: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.c ** Message: 18:15:31.401: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.c ** Message: 18:15:32.294: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 18:15:33.536: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.o] ** Message: 18:15:33.536: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.o ** Message: 18:15:33.541: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score] ** Message: 18:15:33.542: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.o] ** Message: 18:15:33.542: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.o ** Message: 18:15:33.547: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path] ** Message: 18:15:33.547: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.o] ** Message: 18:15:33.547: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.o ** Message: 18:15:33.553: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region] ** Message: 18:15:33.553: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.o] ** Message: 18:15:33.553: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.o ** Message: 18:15:33.559: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint] ** Message: 18:15:33.559: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 18:15:33.559: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 18:15:33.565: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation] ** Message: 18:15:33.565: Bootstrapper processing model [affine:bestfit:protein2protein] ** Message: 18:15:33.566: Process optimal [optimal:affine:bestfit:protein2protein] ** Message: 18:15:33.567: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.c ** Message: 18:15:34.272: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.c ** Message: 18:15:35.780: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.c ** Message: 18:15:37.891: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.c ** Message: 18:15:38.440: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.c ** Message: 18:15:39.310: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.o] ** Message: 18:15:39.310: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.o ** Message: 18:15:39.316: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score] ** Message: 18:15:39.316: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.o] ** Message: 18:15:39.316: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.o ** Message: 18:15:39.322: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path] ** Message: 18:15:39.322: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.o] ** Message: 18:15:39.322: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.o ** Message: 18:15:39.328: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region] ** Message: 18:15:39.328: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.o] ** Message: 18:15:39.328: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.o ** Message: 18:15:39.334: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint] ** Message: 18:15:39.334: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.o] ** Message: 18:15:39.334: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.o ** Message: 18:15:39.340: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation] ** Message: 18:15:39.340: Processing model [a:l] ** Message: 18:15:39.341: Bootstrapper processing model [affine:local:dna2dna] ** Message: 18:15:39.341: Process optimal [optimal:affine:local:dna2dna] ** Message: 18:15:39.341: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.c ** Message: 18:15:39.865: 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_5/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_5/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.c ** Message: 18:15:40.226: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.c ** Message: 18:15:40.701: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.c ** Message: 18:15:42.568: 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_5/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_5/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 18:15:44.274: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.o] ** Message: 18:15:44.274: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.o ** Message: 18:15:44.281: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_score] ** Message: 18:15:44.281: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.o] ** Message: 18:15:44.281: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.o ** Message: 18:15:44.287: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_path] ** Message: 18:15:44.287: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.o] ** Message: 18:15:44.287: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.o ** Message: 18:15:44.293: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_region] ** Message: 18:15:44.293: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o] ** Message: 18:15:44.293: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o ** Message: 18:15:44.299: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint] ** Message: 18:15:44.299: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 18:15:44.299: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 18:15:44.305: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation] ** Message: 18:15:44.307: Process optimal [Terminal [Segment("START"->"match"):[affine:local:dna2dna]]] ** Message: 18:15:44.308: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:15:44.942: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:15:46.109: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:15:46.109: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:15:46.116: 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: 18:15:46.116: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:15:46.116: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:15:46.122: 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: 18:15:46.123: Process optimal [Terminal [Segment("match"->"END"):[affine:local:dna2dna]]] ** Message: 18:15:46.123: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:15:46.915: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:15:47.572: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:15:47.572: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:15:47.579: 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: 18:15:47.580: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:15:47.580: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:15:47.586: 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: 18:15:47.586: Process optimal [HeuristicJoin:[Segment("match"->"match"):[affine:local:dna2dna]]] ** Message: 18:15:47.588: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:15:49.737: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:15:53.575: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:15:53.575: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:15:53.582: 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: 18:15:53.582: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:15:53.582: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:15:53.589: 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: 18:15:53.590: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.c ** Message: 18:15:53.845: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.c ** Message: 18:15:54.322: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.o] ** Message: 18:15:54.322: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.o ** Message: 18:15:54.329: Adding function [Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded] ** Message: 18:15:54.329: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.o] ** Message: 18:15:54.329: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.o ** Message: 18:15:54.335: Adding function [Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded] ** Message: 18:15:54.336: Bootstrapper processing model [affine:local:protein2protein] ** Message: 18:15:54.336: Process optimal [optimal:affine:local:protein2protein] ** Message: 18:15:54.336: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.c ** Message: 18:15:54.724: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.c ** Message: 18:15:55.006: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.c ** Message: 18:15:55.395: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.c ** Message: 18:15:56.474: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.c ** Message: 18:15:58.072: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.o] ** Message: 18:15:58.072: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.o ** Message: 18:15:58.079: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_score] ** Message: 18:15:58.079: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.o] ** Message: 18:15:58.079: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.o ** Message: 18:15:58.087: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_path] ** Message: 18:15:58.087: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.o] ** Message: 18:15:58.087: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.o ** Message: 18:15:58.096: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_region] ** Message: 18:15:58.096: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o] ** Message: 18:15:58.096: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o ** Message: 18:15:58.106: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint] ** Message: 18:15:58.106: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o] ** Message: 18:15:58.106: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o ** Message: 18:15:58.115: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation] ** Message: 18:15:58.117: Process optimal [Terminal [Segment("START"->"match"):[affine:local:protein2protein]]] ** Message: 18:15:58.118: 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_5/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_5/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: 18:15:58.969: 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_5/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_5/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: 18:16:00.461: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:16:00.461: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:16:00.468: 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: 18:16:00.468: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:16:00.468: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:16:00.475: 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: 18:16:00.475: Process optimal [Terminal [Segment("match"->"END"):[affine:local:protein2protein]]] ** Message: 18:16:00.476: 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_5/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_5/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: 18:16:01.203: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:16:02.619: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:16:02.619: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:16:02.627: 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: 18:16:02.627: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:16:02.627: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:16:02.634: 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: 18:16:02.635: Process optimal [HeuristicJoin:[Segment("match"->"match"):[affine:local:protein2protein]]] ** Message: 18:16:02.636: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:16:04.557: 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_5/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_5/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: 18:16:10.491: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:16:10.491: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:16:10.498: 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: 18:16:10.498: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:16:10.498: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:16:10.505: 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: 18:16:10.505: 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_5/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_5/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.c ** Message: 18:16:10.774: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.c ** Message: 18:16:12.042: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.o] ** Message: 18:16:12.042: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.o ** Message: 18:16:12.049: Adding function [Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded] ** Message: 18:16:12.049: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.o] ** Message: 18:16:12.049: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.o ** Message: 18:16:12.057: Adding function [Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded] ** Message: 18:16:12.057: Processing model [a:o] ** Message: 18:16:12.058: Bootstrapper processing model [affine:overlap:dna2dna] ** Message: 18:16:12.058: Process optimal [optimal:affine:overlap:dna2dna] ** Message: 18:16:12.059: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.c ** Message: 18:16:12.960: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.c ** Message: 18:16:14.642: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.c ** Message: 18:16:16.516: 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_5/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_5/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.c ** Message: 18:16:18.027: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 18:16:20.789: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.o] ** Message: 18:16:20.789: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.o ** Message: 18:16:20.797: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score] ** Message: 18:16:20.797: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.o] ** Message: 18:16:20.797: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.o ** Message: 18:16:20.804: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path] ** Message: 18:16:20.804: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.o] ** Message: 18:16:20.804: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.o ** Message: 18:16:20.811: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region] ** Message: 18:16:20.811: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.o] ** Message: 18:16:20.811: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.o ** Message: 18:16:20.818: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint] ** Message: 18:16:20.818: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 18:16:20.818: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 18:16:20.824: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation] ** Message: 18:16:20.824: Processing model [e2g] ** Message: 18:16:20.825: Bootstrapper processing model [est2genome] ** Message: 18:16:20.825: Process optimal [optimal:est2genome] ** Message: 18:16:20.827: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_est2genome_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_est2genome_32_find_32_score.c ** Message: 18:16:25.866: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_est2genome_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_est2genome_32_find_32_path.c ** Message: 18:16:29.796: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_est2genome_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_est2genome_32_find_32_region.c ** Message: 18:16:34.138: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_est2genome_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_est2genome_32_find_32_checkpoint.c ** Message: 18:16:42.858: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_est2genome_32_find_32_path_32_continuation.c ** Message: 18:16:57.565: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_est2genome_32_find_32_score.o] ** Message: 18:16:57.565: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_est2genome_32_find_32_score.o ** Message: 18:16:57.603: Adding function [optimal_58_est2genome_32_find_32_score] ** Message: 18:16:57.603: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_est2genome_32_find_32_path.o] ** Message: 18:16:57.603: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_est2genome_32_find_32_path.o ** Message: 18:16:57.610: Adding function [optimal_58_est2genome_32_find_32_path] ** Message: 18:16:57.610: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_est2genome_32_find_32_region.o] ** Message: 18:16:57.610: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_est2genome_32_find_32_region.o ** Message: 18:16:57.618: Adding function [optimal_58_est2genome_32_find_32_region] ** Message: 18:16:57.618: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_est2genome_32_find_32_checkpoint.o] ** Message: 18:16:57.618: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_est2genome_32_find_32_checkpoint.o ** Message: 18:16:57.631: Adding function [optimal_58_est2genome_32_find_32_checkpoint] ** Message: 18:16:57.631: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_est2genome_32_find_32_path_32_continuation.o] ** Message: 18:16:57.631: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_est2genome_32_find_32_path_32_continuation.o ** Message: 18:16:57.638: Adding function [optimal_58_est2genome_32_find_32_path_32_continuation] ** Message: 18:16:57.646: Process optimal [Terminal [Segment("START"->"match reverse"):[est2genome]]] ** Message: 18:16:57.648: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:17:00.502: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:17:07.105: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:17:07.105: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:17:07.112: 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: 18:17:07.113: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:17:07.113: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:17:07.144: 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: 18:17:07.144: Process optimal [Terminal [Segment("match reverse"->"END"):[est2genome]]] ** Message: 18:17:07.145: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:17:09.708: 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_5/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_5/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: 18:17:12.596: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:17:12.596: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:17:12.605: 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: 18:17:12.605: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:17:12.605: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:17:12.614: 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: 18:17:12.614: Process optimal [Terminal [Segment("START"->"match forward"):[est2genome]]] ** Message: 18:17:12.616: 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_5/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_5/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: 18:17:16.551: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:17:23.568: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:17:23.568: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:17:23.576: 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: 18:17:23.576: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:17:23.576: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:17:23.647: 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: 18:17:23.647: Process optimal [Terminal [Segment("match forward"->"END"):[est2genome]]] ** Message: 18:17:23.648: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:17:25.472: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:17:28.171: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:17:28.171: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:17:28.179: 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: 18:17:28.179: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:17:28.179: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:17:28.207: 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: 18:17:28.207: Process optimal [HeuristicJoin:[Segment("match reverse"->"match reverse"):[est2genome]]] ** Message: 18:17:28.211: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:17:36.797: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:17:52.857: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:17:52.857: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:17:52.865: 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: 18:17:52.865: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:17:52.865: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:17:52.873: 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: 18:17:52.873: Process optimal [Src span [Segment("match reverse"->"intron reverse"):[est2genome]]] ** Message: 18:17:52.875: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:17:55.837: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:17:59.434: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:17:59.434: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:17:59.442: 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: 18:17:59.443: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:17:59.443: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:17:59.461: 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: 18:17:59.461: Process optimal [Src span traceback [Segment("match reverse"->"intron reverse"):[est2genome]]] ** Message: 18:17:59.465: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:18:10.758: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:18:10.758: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:18:10.766: 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: 18:18:10.766: Process optimal [Dst span [Segment("intron reverse"->"match reverse"):[est2genome]]] ** Message: 18:18:10.768: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:18:15.706: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:18:22.269: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:18:22.269: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:18:22.278: 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: 18:18:22.278: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:18:22.278: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:18:22.307: 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: 18:18:22.307: Process optimal [HeuristicJoin:[Segment("match forward"->"match forward"):[est2genome]]] ** Message: 18:18:22.311: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:18:28.910: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:18:43.619: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:18:43.620: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:18:43.628: 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: 18:18:43.628: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:18:43.628: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:18:43.636: 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: 18:18:43.636: Process optimal [Src span [Segment("match forward"->"intron forward"):[est2genome]]] ** Message: 18:18:43.638: 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_5/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_5/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: 18:18:46.021: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:18:49.848: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:18:49.848: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:18:49.856: 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: 18:18:49.856: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:18:49.857: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:18:49.865: 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: 18:18:49.865: Process optimal [Src span traceback [Segment("match forward"->"intron forward"):[est2genome]]] ** Message: 18:18:49.869: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:18:59.474: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:18:59.474: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:18:59.482: 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: 18:18:59.482: Process optimal [Dst span [Segment("intron forward"->"match forward"):[est2genome]]] ** Message: 18:18:59.484: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:19:03.711: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:19:08.991: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:19:08.991: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:19:09.000: 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: 18:19:09.000: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:19:09.000: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:19:09.007: 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: 18:19:09.009: 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_5/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_5/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.c ** Message: 18:19:10.073: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.c ** Message: 18:19:11.133: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.o] ** Message: 18:19:11.133: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.o ** Message: 18:19:11.141: Adding function [Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary] ** Message: 18:19:11.141: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.o] ** Message: 18:19:11.141: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.o ** Message: 18:19:11.150: Adding function [Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary] ** Message: 18:19:11.151: Processing model [ner] ** Message: 18:19:11.151: Bootstrapper processing model [NER:affine:local:dna2dna] ** Message: 18:19:11.151: Process optimal [optimal:NER:affine:local:dna2dna] ** Message: 18:19:11.151: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.c ** Message: 18:19:11.472: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.c ** Message: 18:19:12.894: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.c ** Message: 18:19:13.756: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.c ** Message: 18:19:15.900: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 18:19:17.483: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.o] ** Message: 18:19:17.483: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.o ** Message: 18:19:17.490: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score] ** Message: 18:19:17.490: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.o] ** Message: 18:19:17.490: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.o ** Message: 18:19:17.497: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path] ** Message: 18:19:17.497: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.o] ** Message: 18:19:17.497: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.o ** Message: 18:19:17.503: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region] ** Message: 18:19:17.504: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o] ** Message: 18:19:17.504: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o ** Message: 18:19:17.510: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint] ** Message: 18:19:17.511: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 18:19:17.511: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 18:19:17.518: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation] ** Message: 18:19:17.522: Process optimal [Terminal [Segment("START"->"match"):[NER:affine:local:dna2dna]]] ** Message: 18:19:17.523: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:19:18.576: 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_5/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_5/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: 18:19:20.215: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:19:20.215: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:19:20.224: 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: 18:19:20.224: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:19:20.224: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:19:20.235: 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: 18:19:20.235: Process optimal [Terminal [Segment("match"->"END"):[NER:affine:local:dna2dna]]] ** Message: 18:19:20.236: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:19:21.279: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:19:23.301: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:19:23.301: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:19:23.311: 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: 18:19:23.311: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:19:23.311: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:19:23.320: 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: 18:19:23.320: Process optimal [HeuristicJoin:[Segment("match"->"match"):[NER:affine:local:dna2dna]]] ** Message: 18:19:23.323: 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_5/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_5/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: 18:19:28.421: 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_5/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_5/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: 18:19:36.567: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:19:36.567: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:19:36.577: 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: 18:19:36.577: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:19:36.577: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:19:36.586: 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: 18:19:36.587: Process optimal [Src span [Segment("match"->"ner"):[NER:affine:local:dna2dna]]] ** Message: 18:19:36.588: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:19:37.381: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:19:39.681: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:19:39.681: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:19:39.690: 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: 18:19:39.691: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:19:39.691: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:19:39.701: 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: 18:19:39.702: Process optimal [Src span traceback [Segment("match"->"ner"):[NER:affine:local:dna2dna]]] ** Message: 18:19:39.704: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:19:44.640: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:19:44.640: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:19:44.650: 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: 18:19:44.650: Process optimal [Dst span [Segment("ner"->"match"):[NER:affine:local:dna2dna]]] ** Message: 18:19:44.651: 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_5/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_5/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: 18:19:46.919: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:19:48.954: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:19:48.954: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:19:48.963: 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: 18:19:48.964: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:19:48.964: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:19:48.973: 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: 18:19:48.974: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.c ** Message: 18:19:49.257: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.c ** Message: 18:19:49.589: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.o] ** Message: 18:19:49.589: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.o ** Message: 18:19:49.600: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary] ** Message: 18:19:49.600: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.o] ** Message: 18:19:49.600: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.o ** Message: 18:19:49.610: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary] ** Message: 18:19:49.610: Bootstrapper processing model [NER:affine:local:protein2protein] ** Message: 18:19:49.610: Process optimal [optimal:NER:affine:local:protein2protein] ** Message: 18:19:49.611: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.c ** Message: 18:19:49.880: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.c ** Message: 18:19:50.260: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.c ** Message: 18:19:50.873: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.c ** Message: 18:19:51.911: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.c ** Message: 18:19:53.079: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.o] ** Message: 18:19:53.079: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.o ** Message: 18:19:53.086: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score] ** Message: 18:19:53.086: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.o] ** Message: 18:19:53.087: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.o ** Message: 18:19:53.095: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path] ** Message: 18:19:53.095: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.o] ** Message: 18:19:53.095: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.o ** Message: 18:19:53.104: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region] ** Message: 18:19:53.104: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o] ** Message: 18:19:53.104: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o ** Message: 18:19:53.113: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint] ** Message: 18:19:53.113: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o] ** Message: 18:19:53.113: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o ** Message: 18:19:53.133: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation] ** Message: 18:19:53.136: Process optimal [Terminal [Segment("START"->"match"):[NER:affine:local:protein2protein]]] ** Message: 18:19:53.137: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:19:54.292: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:19:55.956: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:19:55.956: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:19:55.966: 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: 18:19:55.966: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:19:55.966: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:19:55.976: 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: 18:19:55.976: Process optimal [Terminal [Segment("match"->"END"):[NER:affine:local:protein2protein]]] ** Message: 18:19:55.977: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:19:56.595: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:19:57.335: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:19:57.335: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:19:57.345: 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: 18:19:57.345: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:19:57.345: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:19:57.356: 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: 18:19:57.356: Process optimal [HeuristicJoin:[Segment("match"->"match"):[NER:affine:local:protein2protein]]] ** Message: 18:19:57.358: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:20:00.867: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:20:06.780: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:20:06.780: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:20:06.790: 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: 18:20:06.790: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:20:06.790: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:20:06.799: 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: 18:20:06.799: Process optimal [Src span [Segment("match"->"ner"):[NER:affine:local:protein2protein]]] ** Message: 18:20:06.800: 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_5/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_5/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: 18:20:07.401: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:20:08.578: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:20:08.578: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:20:08.588: 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: 18:20:08.588: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:20:08.588: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:20:08.597: 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: 18:20:08.597: Process optimal [Src span traceback [Segment("match"->"ner"):[NER:affine:local:protein2protein]]] ** Message: 18:20:08.599: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:20:12.081: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:20:12.081: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:20:12.091: 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: 18:20:12.091: Process optimal [Dst span [Segment("ner"->"match"):[NER:affine:local:protein2protein]]] ** Message: 18:20:12.093: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:20:13.864: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:20:15.649: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:20:15.649: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:20:15.658: 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: 18:20:15.658: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:20:15.658: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:20:15.669: 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: 18:20:15.670: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.c ** Message: 18:20:15.946: 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_5/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_5/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.c ** Message: 18:20:16.456: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.o] ** Message: 18:20:16.457: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.o ** Message: 18:20:16.467: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary] ** Message: 18:20:16.467: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.o] ** Message: 18:20:16.468: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.o ** Message: 18:20:16.477: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary] ** Message: 18:20:16.478: Processing model [p2d] ** Message: 18:20:16.478: Bootstrapper processing model [protein2dna:local] ** Message: 18:20:16.478: Process optimal [optimal:protein2dna:local] ** Message: 18:20:16.479: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_protein2dna_58_local_32_find_32_score.c ** Message: 18:20:17.118: 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_5/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_5/optimal_58_protein2dna_58_local_32_find_32_path.c ** Message: 18:20:18.101: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_protein2dna_58_local_32_find_32_region.c ** Message: 18:20:19.204: 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_5/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_5/optimal_58_protein2dna_58_local_32_find_32_checkpoint.c ** Message: 18:20:22.112: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.c ** Message: 18:20:27.892: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_protein2dna_58_local_32_find_32_score.o] ** Message: 18:20:27.892: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_protein2dna_58_local_32_find_32_score.o ** Message: 18:20:27.904: Adding function [optimal_58_protein2dna_58_local_32_find_32_score] ** Message: 18:20:27.904: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_protein2dna_58_local_32_find_32_path.o] ** Message: 18:20:27.904: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_protein2dna_58_local_32_find_32_path.o ** Message: 18:20:27.916: Adding function [optimal_58_protein2dna_58_local_32_find_32_path] ** Message: 18:20:27.916: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_protein2dna_58_local_32_find_32_region.o] ** Message: 18:20:27.916: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_protein2dna_58_local_32_find_32_region.o ** Message: 18:20:27.928: Adding function [optimal_58_protein2dna_58_local_32_find_32_region] ** Message: 18:20:27.928: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_protein2dna_58_local_32_find_32_checkpoint.o] ** Message: 18:20:27.928: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_protein2dna_58_local_32_find_32_checkpoint.o ** Message: 18:20:27.940: Adding function [optimal_58_protein2dna_58_local_32_find_32_checkpoint] ** Message: 18:20:27.941: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.o] ** Message: 18:20:27.941: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.o ** Message: 18:20:27.953: Adding function [optimal_58_protein2dna_58_local_32_find_32_path_32_continuation] ** Message: 18:20:27.960: Process optimal [Terminal [Segment("START"->"match"):[protein2dna:local]]] ** Message: 18:20:27.963: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:20:31.183: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:20:36.820: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:20:36.820: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:20:36.831: 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: 18:20:36.831: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:20:36.831: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:20:36.842: 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: 18:20:36.842: Process optimal [Terminal [Segment("match"->"END"):[protein2dna:local]]] ** Message: 18:20:36.843: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:20:39.224: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:20:41.651: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:20:41.651: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:20:41.662: 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: 18:20:41.662: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:20:41.662: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:20:41.672: 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: 18:20:41.672: Process optimal [HeuristicJoin:[Segment("match"->"match"):[protein2dna:local]]] ** Message: 18:20:41.676: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:20:49.003: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:21:00.988: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:21:00.988: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:21:00.999: 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: 18:21:00.999: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:21:00.999: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:21:01.011: 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: 18:21:01.012: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.c ** Message: 18:21:01.298: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.c ** Message: 18:21:01.830: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.o] ** Message: 18:21:01.830: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.o ** Message: 18:21:01.841: Adding function [Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded] ** Message: 18:21:01.841: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.o] ** Message: 18:21:01.841: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.o ** Message: 18:21:01.854: Adding function [Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded] ** Message: 18:21:01.854: Processing model [p2d:b] ** Message: 18:21:01.855: Bootstrapper processing model [protein2dna:bestfit] ** Message: 18:21:01.855: Process optimal [optimal:protein2dna:bestfit] ** Message: 18:21:01.857: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_protein2dna_58_bestfit_32_find_32_score.c ** Message: 18:21:05.950: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_protein2dna_58_bestfit_32_find_32_path.c ** Message: 18:21:11.739: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_protein2dna_58_bestfit_32_find_32_region.c ** Message: 18:21:16.897: 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_5/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_5/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.c ** Message: 18:21:19.552: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.c ** Message: 18:21:24.099: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_protein2dna_58_bestfit_32_find_32_score.o] ** Message: 18:21:24.099: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_protein2dna_58_bestfit_32_find_32_score.o ** Message: 18:21:24.110: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_score] ** Message: 18:21:24.110: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_protein2dna_58_bestfit_32_find_32_path.o] ** Message: 18:21:24.110: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_protein2dna_58_bestfit_32_find_32_path.o ** Message: 18:21:24.123: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_path] ** Message: 18:21:24.123: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_protein2dna_58_bestfit_32_find_32_region.o] ** Message: 18:21:24.123: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_protein2dna_58_bestfit_32_find_32_region.o ** Message: 18:21:24.134: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_region] ** Message: 18:21:24.134: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.o] ** Message: 18:21:24.134: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.o ** Message: 18:21:24.146: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint] ** Message: 18:21:24.146: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.o] ** Message: 18:21:24.146: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.o ** Message: 18:21:24.159: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation] ** Message: 18:21:24.159: Processing model [p2g] ** Message: 18:21:24.160: Bootstrapper processing model [protein2genome:local] ** Message: 18:21:24.160: Process optimal [optimal:protein2genome:local] ** Message: 18:21:24.161: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_protein2genome_58_local_32_find_32_score.c ** Message: 18:21:26.712: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_protein2genome_58_local_32_find_32_path.c ** Message: 18:21:29.876: 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_5/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_5/optimal_58_protein2genome_58_local_32_find_32_region.c ** Message: 18:21:32.209: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_protein2genome_58_local_32_find_32_checkpoint.c ** Message: 18:21:43.135: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.c ** Message: 18:21:56.722: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_protein2genome_58_local_32_find_32_score.o] ** Message: 18:21:56.722: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_protein2genome_58_local_32_find_32_score.o ** Message: 18:21:56.733: Adding function [optimal_58_protein2genome_58_local_32_find_32_score] ** Message: 18:21:56.733: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_protein2genome_58_local_32_find_32_path.o] ** Message: 18:21:56.733: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_protein2genome_58_local_32_find_32_path.o ** Message: 18:21:56.744: Adding function [optimal_58_protein2genome_58_local_32_find_32_path] ** Message: 18:21:56.744: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_protein2genome_58_local_32_find_32_region.o] ** Message: 18:21:56.744: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_protein2genome_58_local_32_find_32_region.o ** Message: 18:21:56.755: Adding function [optimal_58_protein2genome_58_local_32_find_32_region] ** Message: 18:21:56.755: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_protein2genome_58_local_32_find_32_checkpoint.o] ** Message: 18:21:56.755: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_protein2genome_58_local_32_find_32_checkpoint.o ** Message: 18:21:56.766: Adding function [optimal_58_protein2genome_58_local_32_find_32_checkpoint] ** Message: 18:21:56.766: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.o] ** Message: 18:21:56.766: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.o ** Message: 18:21:56.778: Adding function [optimal_58_protein2genome_58_local_32_find_32_path_32_continuation] ** Message: 18:21:56.806: Process optimal [Terminal [Segment("START"->"match"):[protein2genome:local]]] ** Message: 18:21:56.812: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:22:08.338: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:22:31.955: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:22:31.955: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:22:31.966: 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: 18:22:31.966: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:22:31.966: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:22:31.979: 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: 18:22:31.979: Process optimal [Terminal [Segment("match"->"END"):[protein2genome:local]]] ** Message: 18:22:31.982: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:22:37.935: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:22:50.895: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:22:50.895: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:22:50.908: 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: 18:22:50.909: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:22:50.909: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:22:50.920: 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: 18:22:50.920: Process optimal [HeuristicJoin:[Segment("match"->"match"):[protein2genome:local]]] ** Message: 18:22:50.929: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:23:17.470: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:24:12.421: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:24:12.421: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:24:12.434: 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: 18:24:12.434: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:24:12.434: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:24:12.451: 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: 18:24:12.451: Process optimal [Src span [Segment("match"->"intron 0:0 phase-T"):[protein2genome:local]]] ** Message: 18:24:12.455: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:24:16.903: 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_5/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_5/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: 18:24:24.084: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:24:24.084: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:24:24.100: 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: 18:24:24.100: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:24:24.100: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:24:24.114: 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: 18:24:24.114: Process optimal [Src span traceback [Segment("match"->"intron 0:0 phase-T"):[protein2genome:local]]] ** Message: 18:24:24.123: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:25:07.368: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:25:07.368: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:25:07.382: 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: 18:25:07.382: Process optimal [Dst span [Segment("intron 0:0 phase-T"->"match"):[protein2genome:local]]] ** Message: 18:25:07.387: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:25:25.387: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:25:47.502: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:25:47.502: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:25:47.515: 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: 18:25:47.515: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:25:47.516: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:25:47.530: 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: 18:25:47.530: Process optimal [Src span [Segment("match"->"intron 1:2 phase-T"):[protein2genome:local]]] ** Message: 18:25:47.533: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:25:51.915: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:25:58.663: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:25:58.664: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:25:58.676: 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: 18:25:58.676: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:25:58.676: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:25:58.688: 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: 18:25:58.688: Process optimal [Src span traceback [Segment("match"->"intron 1:2 phase-T"):[protein2genome:local]]] ** Message: 18:25:58.697: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:26:27.117: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:26:27.117: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:26:27.130: 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: 18:26:27.130: Process optimal [Dst span [Segment("intron 1:2 phase-T"->"match"):[protein2genome:local]]] ** Message: 18:26:27.137: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:26:36.066: 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_5/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_5/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: 18:26:48.746: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:26:48.746: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:26:48.758: 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: 18:26:48.758: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:26:48.758: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:26:48.771: 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: 18:26:48.771: Process optimal [Src span [Segment("match"->"intron 2:1 phase-T"):[protein2genome:local]]] ** Message: 18:26:48.775: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:26:51.214: 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_5/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_5/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: 18:26:55.510: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:26:55.510: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:26:55.521: 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: 18:26:55.521: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:26:55.521: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:26:55.534: 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: 18:26:55.534: Process optimal [Src span traceback [Segment("match"->"intron 2:1 phase-T"):[protein2genome:local]]] ** Message: 18:26:55.543: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:27:16.336: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:27:16.336: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:27:16.349: 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: 18:27:16.349: Process optimal [Dst span [Segment("intron 2:1 phase-T"->"match"):[protein2genome:local]]] ** Message: 18:27:16.355: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:27:23.647: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:27:35.489: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:27:35.489: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:27:35.503: 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: 18:27:35.503: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:27:35.503: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:27:35.518: 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: 18:27:35.519: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.c ** Message: 18:27:36.335: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.c ** Message: 18:27:36.820: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.o] ** Message: 18:27:36.820: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.o ** Message: 18:27:36.835: Adding function [Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary] ** Message: 18:27:36.835: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.o] ** Message: 18:27:36.835: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.o ** Message: 18:27:36.850: Adding function [Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary] ** Message: 18:27:36.850: Processing model [p2g:b] ** Message: 18:27:36.851: Bootstrapper processing model [protein2genome:bestfit] ** Message: 18:27:36.851: Process optimal [optimal:protein2genome:bestfit] ** Message: 18:27:36.857: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_protein2genome_58_bestfit_32_find_32_score.c ** Message: 18:27:45.947: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_protein2genome_58_bestfit_32_find_32_path.c ** Message: 18:28:02.755: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_protein2genome_58_bestfit_32_find_32_region.c ** Message: 18:28:20.909: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.c ** Message: 18:28:27.730: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.c ** Message: 18:28:42.497: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_protein2genome_58_bestfit_32_find_32_score.o] ** Message: 18:28:42.497: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_protein2genome_58_bestfit_32_find_32_score.o ** Message: 18:28:42.523: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_score] ** Message: 18:28:42.523: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_protein2genome_58_bestfit_32_find_32_path.o] ** Message: 18:28:42.523: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_protein2genome_58_bestfit_32_find_32_path.o ** Message: 18:28:42.539: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_path] ** Message: 18:28:42.539: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_protein2genome_58_bestfit_32_find_32_region.o] ** Message: 18:28:42.539: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_protein2genome_58_bestfit_32_find_32_region.o ** Message: 18:28:42.554: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_region] ** Message: 18:28:42.554: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.o] ** Message: 18:28:42.554: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.o ** Message: 18:28:42.570: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint] ** Message: 18:28:42.570: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.o] ** Message: 18:28:42.570: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.o ** Message: 18:28:42.585: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation] ** Message: 18:28:42.585: Processing model [c2c] ** Message: 18:28:42.586: Bootstrapper processing model [coding2coding] ** Message: 18:28:42.586: Process optimal [optimal:coding2coding] ** Message: 18:28:42.588: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_coding2coding_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_coding2coding_32_find_32_score.c ** Message: 18:28:44.425: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_coding2coding_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_coding2coding_32_find_32_path.c ** Message: 18:28:48.143: 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_5/optimal_58_coding2coding_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_coding2coding_32_find_32_region.c ** Message: 18:28:50.942: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_coding2coding_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_coding2coding_32_find_32_checkpoint.c ** Message: 18:28:59.339: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_coding2coding_32_find_32_path_32_continuation.c ** Message: 18:29:15.969: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_coding2coding_32_find_32_score.o] ** Message: 18:29:15.969: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_coding2coding_32_find_32_score.o ** Message: 18:29:15.994: Adding function [optimal_58_coding2coding_32_find_32_score] ** Message: 18:29:15.994: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_coding2coding_32_find_32_path.o] ** Message: 18:29:15.994: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_coding2coding_32_find_32_path.o ** Message: 18:29:16.015: Adding function [optimal_58_coding2coding_32_find_32_path] ** Message: 18:29:16.015: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_coding2coding_32_find_32_region.o] ** Message: 18:29:16.015: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_coding2coding_32_find_32_region.o ** Message: 18:29:16.029: Adding function [optimal_58_coding2coding_32_find_32_region] ** Message: 18:29:16.029: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_coding2coding_32_find_32_checkpoint.o] ** Message: 18:29:16.029: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_coding2coding_32_find_32_checkpoint.o ** Message: 18:29:16.046: Adding function [optimal_58_coding2coding_32_find_32_checkpoint] ** Message: 18:29:16.046: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_coding2coding_32_find_32_path_32_continuation.o] ** Message: 18:29:16.046: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_coding2coding_32_find_32_path_32_continuation.o ** Message: 18:29:16.061: Adding function [optimal_58_coding2coding_32_find_32_path_32_continuation] ** Message: 18:29:16.085: Process optimal [Terminal [Segment("START"->"match"):[coding2coding]]] ** Message: 18:29:16.091: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:29:25.527: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:29:47.961: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:29:47.962: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:29:47.977: 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: 18:29:47.977: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:29:47.977: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:29:47.994: 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: 18:29:47.994: Process optimal [Terminal [Segment("match"->"END"):[coding2coding]]] ** Message: 18:29:47.997: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:29:52.596: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:30:00.415: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:30:00.415: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:30:00.430: 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: 18:30:00.430: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:30:00.430: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:30:00.444: 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: 18:30:00.444: Process optimal [HeuristicJoin:[Segment("match"->"match"):[coding2coding]]] ** Message: 18:30:00.452: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:30:23.205: 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_5/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_5/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: 18:31:24.281: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:31:24.281: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:31:24.296: 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: 18:31:24.296: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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: 18:31:24.296: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/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: 18:31:24.310: 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: 18:31:24.331: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.c ** Message: 18:31:24.705: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.c ** Message: 18:31:25.354: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.o] ** Message: 18:31:25.354: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.o ** Message: 18:31:25.370: Adding function [Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded] ** Message: 18:31:25.370: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.o] ** Message: 18:31:25.370: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.o ** Message: 18:31:25.385: Adding function [Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded] ** Message: 18:31:25.385: Processing model [c2g] ** Message: 18:31:25.386: Bootstrapper processing model [coding2genome] ** Message: 18:31:25.386: Process optimal [optimal:coding2genome] ** Message: 18:31:25.390: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_coding2genome_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_coding2genome_32_find_32_score.c ** Message: 18:31:34.544: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_coding2genome_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_coding2genome_32_find_32_path.c ** Message: 18:31:46.838: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_coding2genome_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_coding2genome_32_find_32_region.c ** Message: 18:31:57.167: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_coding2genome_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_coding2genome_32_find_32_checkpoint.c ** Message: 18:32:34.854: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_coding2genome_32_find_32_path_32_continuation.c ** Message: 18:33:34.528: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_coding2genome_32_find_32_score.o] ** Message: 18:33:34.528: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_coding2genome_32_find_32_score.o ** Message: 18:33:34.544: Adding function [optimal_58_coding2genome_32_find_32_score] ** Message: 18:33:34.544: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_coding2genome_32_find_32_path.o] ** Message: 18:33:34.544: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_coding2genome_32_find_32_path.o ** Message: 18:33:34.561: Adding function [optimal_58_coding2genome_32_find_32_path] ** Message: 18:33:34.561: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_coding2genome_32_find_32_region.o] ** Message: 18:33:34.561: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_coding2genome_32_find_32_region.o ** Message: 18:33:34.578: Adding function [optimal_58_coding2genome_32_find_32_region] ** Message: 18:33:34.578: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_coding2genome_32_find_32_checkpoint.o] ** Message: 18:33:34.578: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_coding2genome_32_find_32_checkpoint.o ** Message: 18:33:34.596: Adding function [optimal_58_coding2genome_32_find_32_checkpoint] ** Message: 18:33:34.596: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_coding2genome_32_find_32_path_32_continuation.o] ** Message: 18:33:34.596: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_coding2genome_32_find_32_path_32_continuation.o ** Message: 18:33:34.613: Adding function [optimal_58_coding2genome_32_find_32_path_32_continuation] ** Message: 18:33:34.614: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.c ** Message: 18:33:36.038: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.c ** Message: 18:33:37.302: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.o] ** Message: 18:33:37.302: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.o ** Message: 18:33:37.318: Adding function [Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary] ** Message: 18:33:37.318: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.o] ** Message: 18:33:37.318: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.o ** Message: 18:33:37.333: Adding function [Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary] ** Message: 18:33:37.334: Processing model [cd2g] ** Message: 18:33:37.336: Bootstrapper processing model [cdna2genome] ** Message: 18:33:37.336: Process optimal [optimal:cdna2genome] ** Message: 18:33:37.344: 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_5/optimal_58_cdna2genome_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_cdna2genome_32_find_32_score.c ** Message: 18:33:57.292: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_cdna2genome_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_cdna2genome_32_find_32_path.c ** Message: 18:34:21.970: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_cdna2genome_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_cdna2genome_32_find_32_region.c ** Message: 18:34:46.954: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_cdna2genome_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_cdna2genome_32_find_32_checkpoint.c ** Message: 18:36:38.901: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_cdna2genome_32_find_32_path_32_continuation.c ** Message: 18:39:59.812: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_cdna2genome_32_find_32_score.o] ** Message: 18:39:59.812: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_cdna2genome_32_find_32_score.o ** Message: 18:39:59.829: Adding function [optimal_58_cdna2genome_32_find_32_score] ** Message: 18:39:59.829: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_cdna2genome_32_find_32_path.o] ** Message: 18:39:59.829: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_cdna2genome_32_find_32_path.o ** Message: 18:39:59.845: Adding function [optimal_58_cdna2genome_32_find_32_path] ** Message: 18:39:59.845: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_cdna2genome_32_find_32_region.o] ** Message: 18:39:59.845: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_cdna2genome_32_find_32_region.o ** Message: 18:39:59.861: Adding function [optimal_58_cdna2genome_32_find_32_region] ** Message: 18:39:59.861: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_cdna2genome_32_find_32_checkpoint.o] ** Message: 18:39:59.861: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_cdna2genome_32_find_32_checkpoint.o ** Message: 18:39:59.878: Adding function [optimal_58_cdna2genome_32_find_32_checkpoint] ** Message: 18:39:59.878: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/optimal_58_cdna2genome_32_find_32_path_32_continuation.o] ** Message: 18:39:59.878: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/optimal_58_cdna2genome_32_find_32_path_32_continuation.o ** Message: 18:39:59.896: Adding function [optimal_58_cdna2genome_32_find_32_path_32_continuation] ** Message: 18:39:59.897: 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_5/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_5/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.c ** Message: 18:40:02.796: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.c ** Message: 18:40:04.810: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o] ** Message: 18:40:04.810: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o ** Message: 18:40:04.832: Adding function [Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary] ** Message: 18:40:04.832: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o] ** Message: 18:40:04.833: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_5/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_5/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o ** Message: 18:40:04.851: Adding function [Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary] ** Message: 18:40:04.852: 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: 18:40:05.125: Adding: [c4_model_lookup.o] ** Message: 18:40:05.125: Adding object file [c4_model_lookup.o] to archive ar -Sq c4_model_archive.a c4_model_lookup.o ** Message: 18:40:05.148: Indexing archive [c4_model_archive.a] ranlib c4_model_archive.a ** Message: 18:40:05.187: Done ** Message: 18:40:05.187: 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-dragonfly5.5\"" -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-dragonfly5.5\"" -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-dragonfly5.5\"" -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-dragonfly5.5\"" -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: Thursday, 7 MAR 2019 at 18:40:25 UTC Duration: 00:26:31