------------------------------------------------------------------------------- -- Phase: Environment ------------------------------------------------------------------------------- NO_DEPENDS=1 UNAME_r=5.9 UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=unknown UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 LANG=C HOME=/root USER=root TERM=dumb SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: showconfig ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ENV ------------------------------------------------------------------------------- PKG_CONFIG=pkgconf XDG_DATA_HOME=/construction/biology/exonerate XDG_CONFIG_HOME=/construction/biology/exonerate HOME=/construction/biology/exonerate TMPDIR="/tmp" PATH=/construction/biology/exonerate/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8 CONFIG_SITE=/xports/Templates/config.site lt_cv_sys_max_cmd_len=262144 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ARGS ------------------------------------------------------------------------------- --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ENV ------------------------------------------------------------------------------- XDG_DATA_HOME=/construction/biology/exonerate XDG_CONFIG_HOME=/construction/biology/exonerate HOME=/construction/biology/exonerate TMPDIR="/tmp" PATH=/construction/biology/exonerate/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc80 LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8 PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ARGS ------------------------------------------------------------------------------- DESTDIR=/construction/biology/exonerate/stage SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: PLIST_SUB ------------------------------------------------------------------------------- GTK2_VERSION="2.10.0" GTK3_VERSION="3.0.0" OSREL=5.9 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/exonerate" EXAMPLESDIR="share/examples/exonerate" DATADIR="share/exonerate" WWWDIR="www/exonerate" ETCDIR="etc/exonerate" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: SUB_LIST ------------------------------------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/exonerate DOCSDIR=/usr/local/share/doc/exonerate EXAMPLESDIR=/usr/local/share/examples/exonerate WWWDIR=/usr/local/www/exonerate ETCDIR=/usr/local/etc/exonerate SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: /etc/make.conf ------------------------------------------------------------------------------- DPORTS_BUILDER=yes DISABLE_LICENSES=yes DEFAULT_VERSIONS=ssl=openssl FORCE_PACKAGE=yes DEVELOPER=yes USE_PACKAGE_DEPENDS_ONLY=yes PORTSDIR=/xports PORT_DBDIR=/options PKG_DBDIR=/var/db/pkg PKG_CACHEDIR=/var/cache/pkg PKG_SUFX=.txz DEVELOPER=1 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500908 OSVERSION=9999999 OSREL=5.9 _OSRELEASE=5.9-SYNTH DISTDIR=/distfiles WRKDIRPREFIX=/construction BATCH=yes PACKAGE_BUILDING=yes PKG_CREATE_VERBOSE=yes MAKE_JOBS_NUMBER=10 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/pkgconf-1.7.3,1.txz Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/libffi-3.3_1.txz Installing /packages/All/pcre-8.44.txz Installing /packages/All/gettext-runtime-0.21.txz Installing /packages/All/libxml2-2.9.10_3.txz Installing /packages/All/libiconv-1.16.txz Installing /packages/All/expat-2.2.10.txz Installing /packages/All/ncurses-6.2.20210213.txz Installing /packages/All/readline-8.1.0.txz Installing /packages/All/openssl-1.1.1j_1,1.txz Installing /packages/All/python37-3.7.9_1.txz ===== Message from python37-3.7.9_1: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py37-gdbm databases/py-gdbm@py37 py37-sqlite3 databases/py-sqlite3@py37 py37-tkinter x11-toolkits/py-tkinter@py37 Installing /packages/All/glib-2.66.7,1.txz No schema files found: doing nothing. SUCCEEDED 00:00:07 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> exonerate-2.4.0 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> exonerate-2.4.0 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by exonerate-2.4.0 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> exonerate-2.4.0 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by exonerate-2.4.0 for building => SHA256 Checksum OK for exonerate-2.4.0.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> exonerate-2.4.0 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by exonerate-2.4.0 for building ===> Extracting for exonerate-2.4.0 => SHA256 Checksum OK for exonerate-2.4.0.tar.gz. Extracted Memory Use: 3.43M SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for exonerate-2.4.0 SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> exonerate-2.4.0 depends on package: pkgconf>=1.3.0_1 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- ===> exonerate-2.4.0 depends on shared library: libglib-2.0.so - found (/usr/local/lib/libglib-2.0.so) ===> exonerate-2.4.0 depends on shared library: libintl.so - found (/usr/local/lib/libintl.so) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> exonerate-2.4.0 depends on package: pkgconf>=1.3.0_1 - found ===> exonerate-2.4.0 depends on shared library: libglib-2.0.so - found (/usr/local/lib/libglib-2.0.so) ===> exonerate-2.4.0 depends on shared library: libintl.so - found (/usr/local/lib/libintl.so) ===> Configuring for exonerate-2.4.0 configure: loading site script /xports/Templates/config.site checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking whether make sets $(MAKE)... yes checking for working aclocal-1.4... missing checking for working autoconf... missing checking for working automake-1.4... missing checking for working autoheader... missing checking for working makeinfo... missing checking for gcc... cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for a BSD-compatible install... /usr/bin/install -c checking whether make sets $(MAKE)... (cached) yes checking for an ANSI C-conforming const... yes checking for inline... inline checking how to run the C preprocessor... cpp checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep checking for ANSI C header files... (cached) yes checking for sys/types.h... (cached) yes checking for sys/stat.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for memory.h... (cached) yes checking for strings.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for unistd.h... (cached) yes checking for limits.h... (cached) yes checking for errno.h... (cached) yes checking for math.h... (cached) yes checking for strings.h... (cached) yes checking for ctype.h... (cached) yes checking for sys/stat.h... (cached) yes checking for sys/types.h... (cached) yes checking for time.h... (cached) yes checking for unistd.h... (cached) yes checking build system type... x86_64-portbld-dragonfly5.9 checking host system type... x86_64-portbld-dragonfly5.9 Set host to x86_64-portbld-dragonfly5.9 x86_64-portbld-dragonfly5.9 Customising build for X86_64 Set source_root_dir to /construction/biology/exonerate/exonerate-2.4.0 ---------------------------------------------------------------- checking for socklen_t... yes checking for pkg-config... /usr/local/bin/pkg-config Using GLIB-2 Turning assertions off Turning paranoid options off Not using options for profiling with gprof Not using options for analysis with gcov Adding support for LARGE FILES (>2Gb) for a 32 bit system Using COMPILED C4 MODELS Installing UTILITIES Using PTHREADS ---------------------------------------------------------------- configure: creating ./config.status config.status: creating Makefile config.status: creating doc/Makefile config.status: creating doc/man/Makefile config.status: creating doc/man/man1/Makefile config.status: creating src/Makefile config.status: creating src/general/Makefile config.status: creating src/sequence/Makefile config.status: creating src/database/Makefile config.status: creating src/struct/Makefile config.status: creating src/comparison/Makefile config.status: creating src/c4/Makefile config.status: creating src/bsdp/Makefile config.status: creating src/sdp/Makefile config.status: creating src/hub/Makefile config.status: creating src/model/Makefile config.status: creating src/program/Makefile config.status: creating src/util/Makefile config.status: creating test/Makefile config.status: creating test/util/Makefile config.status: creating test/ipcress/Makefile config.status: creating test/exonerate/Makefile config.status: creating test/data/Makefile config.status: creating test/data/cdna/Makefile config.status: creating test/data/protein/Makefile SUCCEEDED 00:00:04 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for exonerate-2.4.0 Making all in doc Making all in man Making all in man1 Making all in src Making all in struct cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fsm.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fsm.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c recyclebin.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fsm.test fsm.test.o fsm.o recyclebin.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c matrix.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c matrix.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o matrix.test matrix.test.o matrix.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c pqueue.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c pqueue.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o pqueue.test pqueue.test.o pqueue.o recyclebin.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c slist.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c slist.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o slist.test slist.test.o slist.o recyclebin.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c rangetree.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c rangetree.c rangetree.c: In function 'RangeTree_insert_recent': rangetree.c:151:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] g_tree_traverse(rt->recent_data, RangeTree_insert_recent_collect, ^~~~~~~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:91, from rangetree.h:23, from rangetree.c:18: /usr/local/include/glib-2.0/glib/gtree.h:88:10: note: declared here void g_tree_traverse (GTree *tree, ^~~~~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o rangetree.test rangetree.test.o rangetree.o recyclebin.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c vfsm.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c vfsm.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o vfsm.test vfsm.test.o vfsm.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c recyclebin.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o recyclebin.test recyclebin.test.o recyclebin.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c sparsecache.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c sparsecache.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o sparsecache.test sparsecache.test.o sparsecache.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c dejavu.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c dejavu.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o dejavu.test dejavu.test.o dejavu.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c bitarray.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c bitarray.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o bitarray.test bitarray.test.o bitarray.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c splaytree.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c splaytree.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o splaytree.test splaytree.test.o splaytree.o recyclebin.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c noitree.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c noitree.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o noitree.test noitree.test.o noitree.o recyclebin.o splaytree.o -L/usr/local/lib -lglib-2.0 -lintl Making all in general cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c argument.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c argument.c argument.c: In function 'ArgumentParse_boolean': argument.c:138:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(arg_string, true_string[i])) ^~ In file included from /usr/local/include/glib-2.0/glib.h:82, from argument.h:26, from argument.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ argument.c:140:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(arg_string, false_string[i])) ^~ In file included from /usr/local/include/glib-2.0/glib.h:82, from argument.h:26, from argument.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ argument.c: In function 'main': argument.c:306:13: warning: Deprecated pre-processor symbol if(!g_thread_supported()) ^~~~~~~~~~~~~~~~~ argument.c:307:9: warning: 'g_thread_init' is deprecated [-Wdeprecated-declarations] g_thread_init(NULL); ^~~~~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:111, from argument.h:26, from argument.c:16: /usr/local/include/glib-2.0/glib/deprecated/gthread.h:261:10: note: declared here void g_thread_init (gpointer vtable); ^~~~~~~~~~~~~ argument.c: In function 'Argument_process': argument.c:502:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] g_tree_traverse(arg->option_registry, Argument_set_env_var_func, ^~~~~~~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:91, from argument.h:26, from argument.c:16: /usr/local/include/glib-2.0/glib/gtree.h:88:10: note: declared here void g_tree_traverse (GTree *tree, ^~~~~~~~~~~~~~~ argument.c:559:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] g_tree_traverse(arg->option_registry, ^~~~~~~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:91, from argument.h:26, from argument.c:16: /usr/local/include/glib-2.0/glib/gtree.h:88:10: note: declared here void g_tree_traverse (GTree *tree, ^~~~~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o argument.test argument.test.o argument.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c lineparse.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c lineparse.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o lineparse.test lineparse.test.o lineparse.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c compoundfile.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c compoundfile.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o compoundfile.test compoundfile.test.o compoundfile.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c socket.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c socket.c socket.c: In function 'Socket_send': socket.c:168:13: warning: Deprecated pre-processor symbol, replace with g_string_sprintfa(full_msg, "linecount: %d\n", line_count+1); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ socket.c:169:13: warning: Deprecated pre-processor symbol, replace with g_string_sprintfa(full_msg, "%s", msg); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o socket.test socket.test.o socket.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c jobqueue.test.c jobqueue.test.c: In function 'main': jobqueue.test.c:34:13: warning: Deprecated pre-processor symbol if(!g_thread_supported()) ^~~~~~~~~~~~~~~~~ jobqueue.test.c:35:9: warning: 'g_thread_init' is deprecated [-Wdeprecated-declarations] g_thread_init(NULL); ^~~~~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:111, from jobqueue.h:23, from jobqueue.test.c:17: /usr/local/include/glib-2.0/glib/deprecated/gthread.h:261:10: note: declared here void g_thread_init (gpointer vtable); ^~~~~~~~~~~~~ cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c jobqueue.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o jobqueue.test jobqueue.test.o jobqueue.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c threadref.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c threadref.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o threadref.test threadref.test.o threadref.o -lpthread -L/usr/local/lib -lglib-2.0 -lintl Making all in sequence cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c sequence.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c sequence.c sequence.c: In function 'Sequence_destroy_annotation_tree': sequence.c:97:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] g_tree_traverse(tree, Sequence_destroy_annotation_data, ^~~~~~~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:91, from sequence.h:24, from sequence.c:21: /usr/local/include/glib-2.0/glib/gtree.h:88:10: note: declared here void g_tree_traverse (GTree *tree, ^~~~~~~~~~~~~~~ cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c alphabet.c alphabet.c: In function 'Alphabet_name_get_type': alphabet.c:317:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(name, dna_string[i])) ^~ In file included from /usr/local/include/glib-2.0/glib.h:82, from alphabet.h:24, from alphabet.c:19: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ alphabet.c:320:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(name, protein_string[i])) ^~ In file included from /usr/local/include/glib-2.0/glib.h:82, from alphabet.h:24, from alphabet.c:19: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ alphabet.c:323:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(name, unknown_string[i])) ^~ In file included from /usr/local/include/glib-2.0/glib.h:82, from alphabet.h:24, from alphabet.c:19: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c translate.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c splice.c splice.c: In function 'SplicePredictor_parse_data': splice.c:146:17: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(word, "splice")) ^~ In file included from /usr/local/include/glib-2.0/glib.h:82, from splice.h:23, from splice.c:22: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ splice.c: In function 'SplicePredictor_add_5SS_data': splice.c:195:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if((!path) || (!strlen(path)) || (!g_strcasecmp(path, "primate"))) ^~ In file included from /usr/local/include/glib-2.0/glib.h:82, from splice.h:23, from splice.c:22: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ splice.c: In function 'SplicePredictor_add_3SS_data': splice.c:203:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if((!path) || (!strlen(path)) || (!g_strcasecmp(path, "primate"))) ^~ In file included from /usr/local/include/glib-2.0/glib.h:82, from splice.h:23, from splice.c:22: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o sequence.test sequence.test.o sequence.o alphabet.o translate.o splice.o ../../src/struct/matrix.o ../../src/struct/sparsecache.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c submat.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c submat.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o submat.test submat.test.o submat.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c translate.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o translate.test translate.test.o translate.o ../../src/general/argument.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c splice.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o splice.test splice.test.o splice.o ../../src/struct/matrix.o ../../src/struct/sparsecache.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c alphabet.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o alphabet.test alphabet.test.o alphabet.o ../../src/general/argument.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c codonsubmat.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c codonsubmat.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o codonsubmat.test codonsubmat.test.o codonsubmat.o ../../src/general/argument.o -lm -L/usr/local/lib -lglib-2.0 -lintl Making all in comparison cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c wordhood.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c wordhood.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o wordhood.test wordhood.test.o wordhood.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c hspset.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c hspset.c hspset.c: In function 'HSP_Display_insert': hspset.c:637:9: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] g_strdown(query_str); ^~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:82, from hspset.h:26, from hspset.c:20: /usr/local/include/glib-2.0/glib/gstrfuncs.h:208:23: note: declared here gchar* g_strdown (gchar *string); ^~~~~~~~~ hspset.c:638:9: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] g_strdown(target_str); ^~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:82, from hspset.h:26, from hspset.c:20: /usr/local/include/glib-2.0/glib/gstrfuncs.h:208:23: note: declared here gchar* g_strdown (gchar *string); ^~~~~~~~~ hspset.c:640:9: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] g_strup(query_str); ^~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:82, from hspset.h:26, from hspset.c:20: /usr/local/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here gchar* g_strup (gchar *string); ^~~~~~~ hspset.c:641:9: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] g_strup(target_str); ^~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:82, from hspset.h:26, from hspset.c:20: /usr/local/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here gchar* g_strup (gchar *string); ^~~~~~~ cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c match.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o hspset.test hspset.test.o hspset.o match.o wordhood.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/general/threadref.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c pcr.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c pcr.c pcr.c: In function 'PCR_Match_allocate': pcr.c:31:9: warning: 'g_mem_chunk_alloc' is deprecated [-Wdeprecated-declarations] pcr_match = g_chunk_new(PCR_Match, pcr->match_mem_chunk); ^~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:106, from pcr.h:23, from pcr.c:16: /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:50:17: note: declared here gpointer g_mem_chunk_alloc (GMemChunk *mem_chunk); ^~~~~~~~~~~~~~~~~ pcr.c: In function 'PCR_Probe_create': pcr.c:59:5: warning: 'g_mem_chunk_alloc' is deprecated [-Wdeprecated-declarations] register PCR_Probe *pcr_probe = g_chunk_new(PCR_Probe, ^~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:106, from pcr.h:23, from pcr.c:16: /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:50:17: note: declared here gpointer g_mem_chunk_alloc (GMemChunk *mem_chunk); ^~~~~~~~~~~~~~~~~ pcr.c: In function 'PCR_Probe_destroy': pcr.c:69:5: warning: 'g_mem_chunk_free' is deprecated [-Wdeprecated-declarations] g_mem_chunk_free(pcr->probe_mem_chunk, pcr_probe); ^~~~~~~~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:106, from pcr.h:23, from pcr.c:16: /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:54:17: note: declared here void g_mem_chunk_free (GMemChunk *mem_chunk, ^~~~~~~~~~~~~~~~ pcr.c: In function 'PCR_Sensor_create': pcr.c:155:5: warning: 'g_mem_chunk_alloc' is deprecated [-Wdeprecated-declarations] register PCR_Sensor *pcr_sensor = g_chunk_new(PCR_Sensor, ^~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:106, from pcr.h:23, from pcr.c:16: /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:50:17: note: declared here gpointer g_mem_chunk_alloc (GMemChunk *mem_chunk); ^~~~~~~~~~~~~~~~~ pcr.c: In function 'PCR_Sensor_destroy': pcr.c:174:5: warning: 'g_mem_chunk_free' is deprecated [-Wdeprecated-declarations] g_mem_chunk_free(pcr->sensor_mem_chunk, pcr_sensor); ^~~~~~~~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:106, from pcr.h:23, from pcr.c:16: /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:54:17: note: declared here void g_mem_chunk_free (GMemChunk *mem_chunk, ^~~~~~~~~~~~~~~~ pcr.c: In function 'PCR_Primer_create': pcr.c:252:5: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] g_strup(pcr_primer->forward); ^~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:82, from pcr.h:23, from pcr.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here gchar* g_strup (gchar *string); ^~~~~~~ pcr.c:253:5: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] g_strup(pcr_primer->revcomp); ^~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:82, from pcr.h:23, from pcr.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here gchar* g_strup (gchar *string); ^~~~~~~ pcr.c: In function 'PCR_create': pcr.c:357:5: warning: 'g_mem_chunk_new' is deprecated [-Wdeprecated-declarations] pcr->sensor_mem_chunk = g_mem_chunk_new("PCR_Sensor", ^~~ In file included from /usr/local/include/glib-2.0/glib.h:106, from pcr.h:23, from pcr.c:16: /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:43:17: note: declared here GMemChunk * g_mem_chunk_new (const gchar *name, ^~~~~~~~~~~~~~~ pcr.c:363:5: warning: 'g_mem_chunk_new' is deprecated [-Wdeprecated-declarations] pcr->probe_mem_chunk = g_mem_chunk_new("PCR_Probe", ^~~ In file included from /usr/local/include/glib-2.0/glib.h:106, from pcr.h:23, from pcr.c:16: /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:43:17: note: declared here GMemChunk * g_mem_chunk_new (const gchar *name, ^~~~~~~~~~~~~~~ pcr.c:366:5: warning: 'g_mem_chunk_new' is deprecated [-Wdeprecated-declarations] pcr->match_mem_chunk = g_mem_chunk_new("PCR_Match", ^~~ In file included from /usr/local/include/glib-2.0/glib.h:106, from pcr.h:23, from pcr.c:16: /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:43:17: note: declared here GMemChunk * g_mem_chunk_new (const gchar *name, ^~~~~~~~~~~~~~~ pcr.c: In function 'PCR_destroy': pcr.c:381:5: warning: 'g_mem_chunk_destroy' is deprecated [-Wdeprecated-declarations] g_mem_chunk_destroy(pcr->sensor_mem_chunk); ^~~~~~~~~~~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:106, from pcr.h:23, from pcr.c:16: /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:48:17: note: declared here void g_mem_chunk_destroy (GMemChunk *mem_chunk); ^~~~~~~~~~~~~~~~~~~ pcr.c:383:5: warning: 'g_mem_chunk_destroy' is deprecated [-Wdeprecated-declarations] g_mem_chunk_destroy(pcr->probe_mem_chunk); ^~~~~~~~~~~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:106, from pcr.h:23, from pcr.c:16: /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:48:17: note: declared here void g_mem_chunk_destroy (GMemChunk *mem_chunk); ^~~~~~~~~~~~~~~~~~~ pcr.c:384:5: warning: 'g_mem_chunk_destroy' is deprecated [-Wdeprecated-declarations] g_mem_chunk_destroy(pcr->match_mem_chunk); ^~~~~~~~~~~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:106, from pcr.h:23, from pcr.c:16: /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:48:17: note: declared here void g_mem_chunk_destroy (GMemChunk *mem_chunk); ^~~~~~~~~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o pcr.test pcr.test.o pcr.o wordhood.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/struct/fsm.o ../../src/struct/slist.o ../../src/struct/recyclebin.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c comparison.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c comparison.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o comparison.test comparison.test.o comparison.o hspset.o match.o wordhood.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/struct/recyclebin.o ../../src/struct/pqueue.o ../../src/general/threadref.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c match.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o match.test match.test.o match.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c seeder.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c seeder.c seeder.c: In function 'Seeder_decide_fsm_type': seeder.c:268:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(force_fsm, "none")) ^~ In file included from /usr/local/include/glib-2.0/glib.h:82, from seeder.h:23, from seeder.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ seeder.c:273:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(force_fsm, "normal")) ^~ In file included from /usr/local/include/glib-2.0/glib.h:82, from seeder.h:23, from seeder.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ seeder.c:275:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(force_fsm, "compact")) ^~ In file included from /usr/local/include/glib-2.0/glib.h:82, from seeder.h:23, from seeder.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o seeder.test seeder.test.o seeder.o wordhood.o hspset.o match.o comparison.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/struct/recyclebin.o ../../src/struct/fsm.o ../../src/struct/vfsm.o ../../src/struct/pqueue.o ../../src/general/threadref.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl Making all in database cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastadb.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastadb.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastadb.test fastadb.test.o fastadb.o ../../src/general/compoundfile.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastapipe.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastapipe.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastapipe.test fastapipe.test.o fastapipe.o fastadb.o ../../src/general/compoundfile.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c dataset.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c dataset.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o dataset.test dataset.test.o dataset.o fastadb.o ../../src/general/compoundfile.o ../../src/struct/bitarray.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c index.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c index.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o index.test index.test.o index.o fastadb.o dataset.o ../../src/general/compoundfile.o ../../src/general/threadref.o ../../src/struct/bitarray.o ../../src/struct/vfsm.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/struct/splaytree.o ../../src/struct/noitree.o ../../src/comparison/wordhood.o ../../src/comparison/hspset.o ../../src/comparison/match.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl Making all in c4 cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c region.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c region.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o region.test region.test.o region.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c c4.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c c4.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o c4.test c4.test.o c4.o region.o ../../src/struct/matrix.o ../../src/general/threadref.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c alignment.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c alignment.c alignment.c: In function 'AlignmentView_add_SPLICE_SITE': alignment.c:660:9: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] g_strdown(qy_seq_string); ^~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:82, from ../../src/comparison/match.h:23, from alignment.c:20: /usr/local/include/glib-2.0/glib/gstrfuncs.h:208:23: note: declared here gchar* g_strdown (gchar *string); ^~~~~~~~~ alignment.c:667:9: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] g_strdown(tg_seq_string); ^~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:82, from ../../src/comparison/match.h:23, from alignment.c:20: /usr/local/include/glib-2.0/glib/gstrfuncs.h:208:23: note: declared here gchar* g_strdown (gchar *string); ^~~~~~~~~ alignment.c:677:13: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] g_strdown(qy_seq_string); ^~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:82, from ../../src/comparison/match.h:23, from alignment.c:20: /usr/local/include/glib-2.0/glib/gstrfuncs.h:208:23: note: declared here gchar* g_strdown (gchar *string); ^~~~~~~~~ alignment.c:690:9: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] g_strdown(tg_seq_string); ^~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:82, from ../../src/comparison/match.h:23, from alignment.c:20: /usr/local/include/glib-2.0/glib/gstrfuncs.h:208:23: note: declared here gchar* g_strdown (gchar *string); ^~~~~~~~~ alignment.c: In function 'AlignmentView_add_SPLIT_CODON': alignment.c:987:5: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] g_strup(qy_codon); ^~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:82, from ../../src/comparison/match.h:23, from alignment.c:20: /usr/local/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here gchar* g_strup (gchar *string); ^~~~~~~ alignment.c:988:5: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] g_strup(tg_codon); ^~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:82, from ../../src/comparison/match.h:23, from alignment.c:20: /usr/local/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here gchar* g_strup (gchar *string); ^~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o alignment.test alignment.test.o alignment.o c4.o region.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/general/threadref.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c codegen.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c codegen.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o codegen.test codegen.test.o codegen.o ../../src/general/argument.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c optimal.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c optimal.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c layout.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c viterbi.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c subopt.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c cgutil.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o optimal.test optimal.test.o optimal.o c4.o alignment.o codegen.o region.o layout.o viterbi.o subopt.o cgutil.o ../../src/struct/slist.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/general/threadref.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c layout.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o layout.test layout.test.o layout.o ../../src/struct/matrix.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c viterbi.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o viterbi.test viterbi.test.o viterbi.o c4.o region.o alignment.o codegen.o layout.o subopt.o cgutil.o ../../src/struct/slist.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/general/threadref.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c opair.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c opair.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o opair.test opair.test.o opair.o optimal.o c4.o alignment.o codegen.o region.o layout.o viterbi.o subopt.o cgutil.o ../../src/struct/slist.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/general/threadref.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c subopt.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o subopt.test subopt.test.o subopt.o region.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c cgutil.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o cgutil.test cgutil.test.o cgutil.o codegen.o c4.o region.o ../../src/general/argument.o ../../src/struct/matrix.o ../../src/general/threadref.o -L/usr/local/lib -lglib-2.0 -lintl Making all in bsdp cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c heuristic.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c heuristic.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o heuristic.test heuristic.test.o heuristic.o ../../src/struct/slist.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/c4/c4.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/codegen.o ../../src/c4/region.o ../../src/c4/layout.o ../../src/c4/viterbi.o ../../src/c4/subopt.o ../../src/c4/cgutil.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c bsdp.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c bsdp.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o bsdp.test bsdp.test.o bsdp.o ../../src/general/argument.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c hpair.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c hpair.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c sar.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o hpair.test hpair.test.o hpair.o heuristic.o bsdp.o sar.o ../../src/struct/slist.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/comparison/hspset.o ../../src/comparison/wordhood.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/c4/c4.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/codegen.o ../../src/c4/region.o ../../src/c4/layout.o ../../src/c4/viterbi.o ../../src/c4/subopt.o ../../src/c4/cgutil.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c sar.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o sar.test sar.test.o sar.o heuristic.o ../../src/struct/slist.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/c4/c4.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/codegen.o ../../src/c4/region.o ../../src/c4/layout.o ../../src/c4/viterbi.o ../../src/c4/subopt.o ../../src/c4/cgutil.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl Making all in sdp cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c sdp.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c sdp.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c boundary.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c scheduler.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c lookahead.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c straceback.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o sdp.test sdp.test.o sdp.o boundary.o scheduler.o lookahead.o straceback.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/comparison/hspset.o ../../src/comparison/comparison.o ../../src/comparison/wordhood.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/c4/c4.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/codegen.o ../../src/c4/region.o ../../src/c4/layout.o ../../src/c4/viterbi.o ../../src/c4/subopt.o ../../src/c4/cgutil.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c lookahead.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o lookahead.test lookahead.test.o lookahead.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c boundary.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o boundary.test boundary.test.o boundary.o ../../src/general/argument.o ../../src/c4/region.o -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c scheduler.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o scheduler.test scheduler.test.o scheduler.o lookahead.o boundary.o straceback.o ../../src/struct/recyclebin.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/c4/c4.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/codegen.o ../../src/c4/region.o ../../src/c4/layout.o ../../src/c4/viterbi.o ../../src/c4/subopt.o ../../src/c4/cgutil.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c straceback.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o straceback.test straceback.test.o straceback.o ../../src/struct/recyclebin.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/c4/c4.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/codegen.o ../../src/c4/region.o ../../src/c4/layout.o ../../src/c4/viterbi.o ../../src/c4/subopt.o ../../src/c4/cgutil.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl Making all in model cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c edit_distance.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c edit_distance.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o edit_distance.test edit_distance.test.o edit_distance.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c affine.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c affine.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c ungapped.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o affine.test affine.test.o affine.o ungapped.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c protein2dna.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c protein2dna.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c frameshift.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o protein2dna.test protein2dna.test.o protein2dna.o affine.o ungapped.o frameshift.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c ner.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c ner.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o ner.test ner.test.o ner.o affine.o ungapped.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c est2genome.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c est2genome.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c intron.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o est2genome.test est2genome.test.o est2genome.o affine.o ungapped.o intron.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c ungapped.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o ungapped.test ungapped.test.o ungapped.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c intron.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o intron.test intron.test.o intron.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c protein2genome.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c protein2genome.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c phase.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o protein2genome.test protein2genome.test.o protein2genome.o protein2dna.o ungapped.o intron.o affine.o frameshift.o phase.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c coding2coding.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c coding2coding.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o coding2coding.test coding2coding.test.o coding2coding.o affine.o ungapped.o frameshift.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c frameshift.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o frameshift.test frameshift.test.o frameshift.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c coding2genome.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c coding2genome.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o coding2genome.test coding2genome.test.o coding2genome.o coding2coding.o affine.o ungapped.o frameshift.o intron.o phase.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c cdna2genome.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c cdna2genome.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o cdna2genome.test cdna2genome.test.o cdna2genome.o affine.o ungapped.o frameshift.o intron.o phase.o coding2coding.o coding2genome.o est2genome.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c genome2genome.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c genome2genome.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o genome2genome.test genome2genome.test.o genome2genome.o coding2coding.o affine.o ungapped.o frameshift.o intron.o phase.o coding2genome.o cdna2genome.o est2genome.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c phase.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o phase.test phase.test.o phase.o intron.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c modeltype.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c modeltype.c modeltype.c: In function 'Model_Type_from_string': modeltype.c:121:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(name[i], str)) ^~ In file included from /usr/local/include/glib-2.0/glib.h:82, from ../../src/c4/c4.h:23, from modeltype.h:23, from modeltype.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ modeltype.c:124:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(short_name[i], str)) ^~ In file included from /usr/local/include/glib-2.0/glib.h:82, from ../../src/c4/c4.h:23, from modeltype.h:23, from modeltype.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o modeltype.test modeltype.test.o modeltype.o ungapped.o affine.o est2genome.o ner.o protein2dna.o protein2genome.o coding2coding.o coding2genome.o genome2genome.o cdna2genome.o frameshift.o phase.o intron.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include \"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c bootstrapper.c bootstrapper.c: In function 'Argument_main': bootstrapper.c:421:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if((!models) || (!g_strcasecmp(models, "all"))) ^~ In file included from /usr/local/include/glib-2.0/glib.h:82, from ../../src/c4/c4.h:23, from ungapped.h:23, from bootstrapper.c:20: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o bootstrapper bootstrapper.o modeltype.o ungapped.o affine.o est2genome.o ner.o protein2dna.o protein2genome.o coding2coding.o coding2genome.o genome2genome.o cdna2genome.o frameshift.o intron.o phase.o ../../src/struct/pqueue.o ../../src/comparison/comparison.o ../../src/comparison/hspset.o ../../src/comparison/wordhood.o ../../src/bsdp/heuristic.o ../../src/sdp/sdp.o ../../src/sdp/scheduler.o ../../src/sdp/straceback.o ../../src/sdp/lookahead.o ../../src/sdp/boundary.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl Making all in hub cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/general -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c gam.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/general -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c gam.c gam.c: In function 'GAM_Refinement_from_string': gam.c:68:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(name[i], str)) ^~ In file included from /usr/local/include/glib-2.0/glib.h:82, from gam.h:23, from gam.c:21: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ gam.c: In function 'GAM_bestn_tree_destroy': gam.c:526:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] g_tree_traverse(bestn_tree, GAM_tree_collect_values, ^~~~~~~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:91, from gam.h:23, from gam.c:21: /usr/local/include/glib-2.0/glib/gtree.h:88:10: note: declared here void g_tree_traverse (GTree *tree, ^~~~~~~~~~~~~~~ gam.c: In function 'GAM_percent_threshold_tree_destroy': gam.c:539:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] g_tree_traverse(percent_threshold_tree, GAM_tree_collect_values, ^~~~~~~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:91, from gam.h:23, from gam.c:21: /usr/local/include/glib-2.0/glib/gtree.h:88:10: note: declared here void g_tree_traverse (GTree *tree, ^~~~~~~~~~~~~~~ gam.c: In function 'GAM_report': gam.c:589:9: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] g_tree_traverse(gam->bestn_tree, GAM_bestn_tree_report_traverse, ^~~~~~~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:91, from gam.h:23, from gam.c:21: /usr/local/include/glib-2.0/glib/gtree.h:88:10: note: declared here void g_tree_traverse (GTree *tree, ^~~~~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o gam.test gam.test.o gam.o ../../src/comparison/hspset.o ../../src/comparison/comparison.o ../../src/comparison/wordhood.o ../../src/struct/sparsecache.o ../../src/general/compoundfile.o ../../src/general/threadref.o ../../src/c4/c4.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/opair.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/region.o ../../src/c4/subopt.o ../../src/bsdp/bsdp.o ../../src/bsdp/sar.o ../../src/bsdp/heuristic.o ../../src/bsdp/hpair.o ../../src/sdp/boundary.o ../../src/sdp/sdp.o ../../src/sdp/scheduler.o ../../src/sdp/straceback.o ../../src/sdp/lookahead.o ../../src/struct/matrix.o ../../src/struct/slist.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/translate.o ../../src/sequence/splice.o ../../src/model/affine.o ../../src/model/est2genome.o ../../src/model/ner.o ../../src/model/protein2dna.o ../../src/model/protein2genome.o ../../src/model/coding2coding.o ../../src/model/coding2genome.o ../../src/model/cdna2genome.o ../../src/model/genome2genome.o ../../src/model/ungapped.o ../../src/model/intron.o ../../src/model/frameshift.o ../../src/model/phase.o ../../src/model/modeltype.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/jobqueue.o ../../src/comparison/match.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/general -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c analysis.test.c cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/general -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c analysis.c analysis.c: In function 'Analysis_decide_scan_query': analysis.c:329:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(force_scan, "none")){ ^~ In file included from /usr/local/include/glib-2.0/glib.h:82, from analysis.h:23, from analysis.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ analysis.c:336:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] } else if((!g_strcasecmp(force_scan, "query")) ^ In file included from /usr/local/include/glib-2.0/glib.h:82, from analysis.h:23, from analysis.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ analysis.c:337:12: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] || (!g_strcasecmp(force_scan, "q"))){ ^~ In file included from /usr/local/include/glib-2.0/glib.h:82, from analysis.h:23, from analysis.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ analysis.c:339:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] } else if((!g_strcasecmp(force_scan, "target")) ^ In file included from /usr/local/include/glib-2.0/glib.h:82, from analysis.h:23, from analysis.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ analysis.c:340:12: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] || (!g_strcasecmp(force_scan, "t"))){ ^~ In file included from /usr/local/include/glib-2.0/glib.h:82, from analysis.h:23, from analysis.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/general -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c bsam.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o analysis.test analysis.test.o analysis.o gam.o bsam.o ../../src/comparison/hspset.o ../../src/comparison/wordhood.o ../../src/comparison/seeder.o ../../src/comparison/comparison.o ../../src/database/fastapipe.o ../../src/database/fastadb.o ../../src/struct/dejavu.o ../../src/struct/fsm.o ../../src/struct/vfsm.o ../../src/struct/sparsecache.o ../../src/general/compoundfile.o ../../src/general/socket.o ../../src/general/threadref.o ../../src/c4/c4.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/opair.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/region.o ../../src/c4/subopt.o ../../src/bsdp/bsdp.o ../../src/bsdp/sar.o ../../src/bsdp/heuristic.o ../../src/bsdp/hpair.o ../../src/sdp/boundary.o ../../src/sdp/sdp.o ../../src/sdp/scheduler.o ../../src/sdp/straceback.o ../../src/sdp/lookahead.o ../../src/struct/matrix.o ../../src/struct/slist.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/translate.o ../../src/sequence/splice.o ../../src/model/affine.o ../../src/model/est2genome.o ../../src/model/ner.o ../../src/model/protein2dna.o ../../src/model/protein2genome.o ../../src/model/coding2coding.o ../../src/model/coding2genome.o ../../src/model/cdna2genome.o ../../src/model/genome2genome.o ../../src/model/ungapped.o ../../src/model/intron.o ../../src/model/frameshift.o ../../src/model/phase.o ../../src/model/modeltype.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/jobqueue.o ../../src/comparison/match.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/general -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c bsam.test.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o bsam.test bsam.test.o bsam.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o ../../src/comparison/hspset.o ../../src/comparison/comparison.o ../../src/comparison/match.o ../../src/comparison/wordhood.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/translate.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/sequence/splice.o ../../src/struct/dejavu.o ../../src/struct/pqueue.o ../../src/struct/sparsecache.o ../../src/struct/recyclebin.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl Making all in program cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/hub -I../../src/general -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c exonerate.c ../../src/model/bootstrapper --compiled no ** Message: 05:09:02.381: Starting building bootstrapping components ** Message: 05:09:02.382: Processing model [u] ** Message: 05:09:02.383: Bootstrapper processing model [ungapped:dna2dna] ** Message: 05:09:02.383: Process optimal [optimal:ungapped:dna2dna] ** (process:294745): WARNING **: 05:09:02.383: Creating codegen directory [/construction/biology/exonerate/exonerate-2.4.0/codegen] ** (process:294745): WARNING **: 05:09:02.383: Creating codegen directory [/construction/biology/exonerate/exonerate-2.4.0/codegen] ** (process:294745): WARNING **: 05:09:02.383: Creating codegen directory [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9] ** (process:294745): WARNING **: 05:09:02.383: Creating codegen directory [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9] ** Message: 05:09:02.384: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2dna_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2dna_32_find_32_score.c ** Message: 05:09:02.627: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2dna_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2dna_32_find_32_path.c ** Message: 05:09:02.911: 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_9/optimal_58_ungapped_58_dna2dna_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2dna_32_find_32_region.c ** Message: 05:09:03.212: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.c ** Message: 05:09:03.528: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 05:09:03.937: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2dna_32_find_32_score.o] ** Message: 05:09:03.937: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2dna_32_find_32_score.o] to archive ar -cSq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2dna_32_find_32_score.o ** Message: 05:09:03.944: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_score] ** Message: 05:09:03.944: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2dna_32_find_32_path.o] ** Message: 05:09:03.944: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2dna_32_find_32_path.o ** Message: 05:09:03.949: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_path] ** Message: 05:09:03.949: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2dna_32_find_32_region.o] ** Message: 05:09:03.950: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2dna_32_find_32_region.o ** Message: 05:09:03.954: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_region] ** Message: 05:09:03.954: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.o] ** Message: 05:09:03.954: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.o ** Message: 05:09:03.958: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint] ** Message: 05:09:03.958: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 05:09:03.958: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 05:09:03.962: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation] ** Message: 05:09:03.962: Bootstrapper processing model [ungapped:protein2protein] ** Message: 05:09:03.962: Process optimal [optimal:ungapped:protein2protein] ** Message: 05:09:03.963: 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_9/optimal_58_ungapped_58_protein2protein_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2protein_32_find_32_score.c ** Message: 05:09:04.179: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2protein_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2protein_32_find_32_path.c ** Message: 05:09:04.440: 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_9/optimal_58_ungapped_58_protein2protein_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2protein_32_find_32_region.c ** Message: 05:09:04.706: 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_9/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.c ** Message: 05:09:05.061: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.c ** Message: 05:09:05.427: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2protein_32_find_32_score.o] ** Message: 05:09:05.427: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2protein_32_find_32_score.o ** Message: 05:09:05.433: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_score] ** Message: 05:09:05.433: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2protein_32_find_32_path.o] ** Message: 05:09:05.433: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2protein_32_find_32_path.o ** Message: 05:09:05.438: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_path] ** Message: 05:09:05.438: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2protein_32_find_32_region.o] ** Message: 05:09:05.439: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2protein_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2protein_32_find_32_region.o ** Message: 05:09:05.444: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_region] ** Message: 05:09:05.444: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.o] ** Message: 05:09:05.444: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.o ** Message: 05:09:05.449: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint] ** Message: 05:09:05.449: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.o] ** Message: 05:09:05.449: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.o ** Message: 05:09:05.454: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation] ** Message: 05:09:05.454: Bootstrapper processing model [ungapped:dna2protein] ** Message: 05:09:05.454: Process optimal [optimal:ungapped:dna2protein] ** Message: 05:09:05.455: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2protein_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2protein_32_find_32_score.c ** Message: 05:09:05.772: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2protein_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2protein_32_find_32_path.c ** Message: 05:09:06.092: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2protein_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2protein_32_find_32_region.c ** Message: 05:09:06.449: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.c ** Message: 05:09:07.270: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.c ** Message: 05:09:07.653: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2protein_32_find_32_score.o] ** Message: 05:09:07.660: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2protein_32_find_32_score.o ** Message: 05:09:07.666: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_score] ** Message: 05:09:07.667: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2protein_32_find_32_path.o] ** Message: 05:09:07.667: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2protein_32_find_32_path.o ** Message: 05:09:07.674: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_path] ** Message: 05:09:07.674: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2protein_32_find_32_region.o] ** Message: 05:09:07.674: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2protein_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2protein_32_find_32_region.o ** Message: 05:09:07.680: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_region] ** Message: 05:09:07.680: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.o] ** Message: 05:09:07.680: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.o ** Message: 05:09:07.685: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint] ** Message: 05:09:07.685: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.o] ** Message: 05:09:07.685: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.o ** Message: 05:09:07.694: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation] ** Message: 05:09:07.694: Bootstrapper processing model [ungapped:protein2dna] ** Message: 05:09:07.694: Process optimal [optimal:ungapped:protein2dna] ** Message: 05:09:07.694: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2dna_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2dna_32_find_32_score.c ** Message: 05:09:08.005: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2dna_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2dna_32_find_32_path.c ** Message: 05:09:08.334: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2dna_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2dna_32_find_32_region.c ** Message: 05:09:08.701: 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_9/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.c ** Message: 05:09:09.299: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.c ** Message: 05:09:09.830: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2dna_32_find_32_score.o] ** Message: 05:09:09.830: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2dna_32_find_32_score.o ** Message: 05:09:09.836: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_score] ** Message: 05:09:09.836: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2dna_32_find_32_path.o] ** Message: 05:09:09.836: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2dna_32_find_32_path.o ** Message: 05:09:09.840: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_path] ** Message: 05:09:09.840: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2dna_32_find_32_region.o] ** Message: 05:09:09.840: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2dna_32_find_32_region.o ** Message: 05:09:09.844: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_region] ** Message: 05:09:09.844: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.o] ** Message: 05:09:09.845: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.o ** Message: 05:09:09.849: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint] ** Message: 05:09:09.849: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.o] ** Message: 05:09:09.849: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.o ** Message: 05:09:09.856: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation] ** Message: 05:09:09.857: Processing model [u:t] ** Message: 05:09:09.857: Bootstrapper processing model [ungapped:codon] ** Message: 05:09:09.857: Process optimal [optimal:ungapped:codon] ** Message: 05:09:09.858: 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_9/optimal_58_ungapped_58_codon_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_codon_32_find_32_score.c ** Message: 05:09:10.269: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_codon_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_codon_32_find_32_path.c ** Message: 05:09:10.764: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_codon_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_codon_32_find_32_region.c ** Message: 05:09:11.240: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_codon_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_codon_32_find_32_checkpoint.c ** Message: 05:09:11.968: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.c ** Message: 05:09:12.855: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_codon_32_find_32_score.o] ** Message: 05:09:12.855: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_codon_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_codon_32_find_32_score.o ** Message: 05:09:12.862: Adding function [optimal_58_ungapped_58_codon_32_find_32_score] ** Message: 05:09:12.862: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_codon_32_find_32_path.o] ** Message: 05:09:12.862: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_codon_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_codon_32_find_32_path.o ** Message: 05:09:12.869: Adding function [optimal_58_ungapped_58_codon_32_find_32_path] ** Message: 05:09:12.870: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_codon_32_find_32_region.o] ** Message: 05:09:12.870: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_codon_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_codon_32_find_32_region.o ** Message: 05:09:12.876: Adding function [optimal_58_ungapped_58_codon_32_find_32_region] ** Message: 05:09:12.876: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_codon_32_find_32_checkpoint.o] ** Message: 05:09:12.876: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_codon_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_codon_32_find_32_checkpoint.o ** Message: 05:09:12.886: Adding function [optimal_58_ungapped_58_codon_32_find_32_checkpoint] ** Message: 05:09:12.886: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.o] ** Message: 05:09:12.886: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.o ** Message: 05:09:12.893: Adding function [optimal_58_ungapped_58_codon_32_find_32_path_32_continuation] ** Message: 05:09:12.893: Processing model [a:g] ** Message: 05:09:12.893: Bootstrapper processing model [affine:global:dna2dna] ** Message: 05:09:12.893: Process optimal [optimal:affine:global:dna2dna] ** Message: 05:09:12.895: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.c ** Message: 05:09:13.503: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.c ** Message: 05:09:14.342: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.c ** Message: 05:09:15.013: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 05:09:15.804: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.o] ** Message: 05:09:15.804: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.o ** Message: 05:09:15.809: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_score] ** Message: 05:09:15.809: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.o] ** Message: 05:09:15.809: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.o ** Message: 05:09:15.815: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_path] ** Message: 05:09:15.815: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.o] ** Message: 05:09:15.815: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.o ** Message: 05:09:15.819: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint] ** Message: 05:09:15.820: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 05:09:15.820: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 05:09:15.824: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation] ** Message: 05:09:15.825: Bootstrapper processing model [affine:global:protein2protein] ** Message: 05:09:15.825: Process optimal [optimal:affine:global:protein2protein] ** Message: 05:09:15.826: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.c ** Message: 05:09:16.258: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.c ** Message: 05:09:16.839: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.c ** Message: 05:09:17.319: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.c ** Message: 05:09:18.186: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.o] ** Message: 05:09:18.186: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.o ** Message: 05:09:18.192: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_score] ** Message: 05:09:18.192: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.o] ** Message: 05:09:18.192: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.o ** Message: 05:09:18.200: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_path] ** Message: 05:09:18.200: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.o] ** Message: 05:09:18.200: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.o ** Message: 05:09:18.207: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint] ** Message: 05:09:18.207: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.o] ** Message: 05:09:18.208: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.o ** Message: 05:09:18.215: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation] ** Message: 05:09:18.215: Processing model [a:b] ** Message: 05:09:18.216: Bootstrapper processing model [affine:bestfit:dna2dna] ** Message: 05:09:18.216: Process optimal [optimal:affine:bestfit:dna2dna] ** Message: 05:09:18.217: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.c ** Message: 05:09:18.921: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.c ** Message: 05:09:20.001: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.c ** Message: 05:09:20.907: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.c ** Message: 05:09:21.674: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 05:09:22.425: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.o] ** Message: 05:09:22.425: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.o ** Message: 05:09:22.433: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score] ** Message: 05:09:22.433: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.o] ** Message: 05:09:22.433: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.o ** Message: 05:09:22.441: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path] ** Message: 05:09:22.441: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.o] ** Message: 05:09:22.441: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.o ** Message: 05:09:22.450: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region] ** Message: 05:09:22.450: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.o] ** Message: 05:09:22.450: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.o ** Message: 05:09:22.457: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint] ** Message: 05:09:22.457: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 05:09:22.457: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 05:09:22.465: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation] ** Message: 05:09:22.466: Bootstrapper processing model [affine:bestfit:protein2protein] ** Message: 05:09:22.466: Process optimal [optimal:affine:bestfit:protein2protein] ** Message: 05:09:22.468: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.c ** Message: 05:09:23.244: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.c ** Message: 05:09:24.464: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.c ** Message: 05:09:25.393: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.c ** Message: 05:09:25.985: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.c ** Message: 05:09:26.779: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.o] ** Message: 05:09:26.779: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.o ** Message: 05:09:26.786: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score] ** Message: 05:09:26.787: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.o] ** Message: 05:09:26.787: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.o ** Message: 05:09:26.795: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path] ** Message: 05:09:26.795: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.o] ** Message: 05:09:26.795: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.o ** Message: 05:09:26.802: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region] ** Message: 05:09:26.802: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.o] ** Message: 05:09:26.802: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.o ** Message: 05:09:26.810: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint] ** Message: 05:09:26.810: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.o] ** Message: 05:09:26.810: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.o ** Message: 05:09:26.818: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation] ** Message: 05:09:26.818: Processing model [a:l] ** Message: 05:09:26.819: Bootstrapper processing model [affine:local:dna2dna] ** Message: 05:09:26.819: Process optimal [optimal:affine:local:dna2dna] ** Message: 05:09:26.821: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.c ** Message: 05:09:27.140: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.c ** Message: 05:09:27.576: 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_9/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.c ** Message: 05:09:28.010: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.c ** Message: 05:09:28.778: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 05:09:29.611: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.o] ** Message: 05:09:29.611: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.o ** Message: 05:09:29.617: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_score] ** Message: 05:09:29.617: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.o] ** Message: 05:09:29.617: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.o ** Message: 05:09:29.623: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_path] ** Message: 05:09:29.623: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.o] ** Message: 05:09:29.623: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.o ** Message: 05:09:29.628: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_region] ** Message: 05:09:29.628: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o] ** Message: 05:09:29.629: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o ** Message: 05:09:29.634: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint] ** Message: 05:09:29.634: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 05:09:29.634: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 05:09:29.640: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation] ** Message: 05:09:29.642: Process optimal [Terminal [Segment("START"->"match"):[affine:local:dna2dna]]] ** Message: 05:09:29.643: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.c ** Message: 05:09:30.060: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.c ** Message: 05:09:30.909: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] ** Message: 05:09:30.909: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o ** Message: 05:09:30.916: 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: 05:09:30.917: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 05:09:30.917: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 05:09:30.924: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path] ** Message: 05:09:30.924: Process optimal [Terminal [Segment("match"->"END"):[affine:local:dna2dna]]] ** Message: 05:09:30.925: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.c ** Message: 05:09:31.317: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.c ** Message: 05:09:31.778: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] ** Message: 05:09:31.778: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o ** Message: 05:09:31.784: 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: 05:09:31.784: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 05:09:31.784: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 05:09:31.790: 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: 05:09:31.790: Process optimal [HeuristicJoin:[Segment("match"->"match"):[affine:local:dna2dna]]] ** Message: 05:09:31.792: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.c ** Message: 05:09:33.063: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.c ** Message: 05:09:34.501: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] ** Message: 05:09:34.501: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o ** Message: 05:09:34.507: 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: 05:09:34.507: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 05:09:34.507: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 05:09:34.514: 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: 05:09:34.515: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.c ** Message: 05:09:34.798: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.c ** Message: 05:09:35.019: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.o] ** Message: 05:09:35.019: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.o ** Message: 05:09:35.026: Adding function [Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded] ** Message: 05:09:35.026: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.o] ** Message: 05:09:35.026: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.o ** Message: 05:09:35.033: Adding function [Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded] ** Message: 05:09:35.033: Bootstrapper processing model [affine:local:protein2protein] ** Message: 05:09:35.033: Process optimal [optimal:affine:local:protein2protein] ** Message: 05:09:35.034: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.c ** Message: 05:09:35.252: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.c ** Message: 05:09:35.525: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.c ** Message: 05:09:35.861: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.c ** Message: 05:09:36.468: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.c ** Message: 05:09:37.161: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.o] ** Message: 05:09:37.161: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.o ** Message: 05:09:37.169: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_score] ** Message: 05:09:37.169: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.o] ** Message: 05:09:37.169: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.o ** Message: 05:09:37.177: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_path] ** Message: 05:09:37.177: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.o] ** Message: 05:09:37.177: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.o ** Message: 05:09:37.185: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_region] ** Message: 05:09:37.185: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o] ** Message: 05:09:37.185: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o ** Message: 05:09:37.195: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint] ** Message: 05:09:37.195: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o] ** Message: 05:09:37.195: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o ** Message: 05:09:37.202: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation] ** Message: 05:09:37.205: Process optimal [Terminal [Segment("START"->"match"):[affine:local:protein2protein]]] ** Message: 05:09:37.207: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.c ** Message: 05:09:37.870: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.c ** Message: 05:09:38.882: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] ** Message: 05:09:38.882: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o ** Message: 05:09:38.891: 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: 05:09:38.891: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 05:09:38.891: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 05:09:38.900: 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: 05:09:38.901: Process optimal [Terminal [Segment("match"->"END"):[affine:local:protein2protein]]] ** Message: 05:09:38.902: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.c ** Message: 05:09:39.423: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.c ** Message: 05:09:39.969: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] ** Message: 05:09:39.969: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o ** Message: 05:09:39.978: 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: 05:09:39.978: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 05:09:39.978: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 05:09:39.987: 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: 05:09:39.987: Process optimal [HeuristicJoin:[Segment("match"->"match"):[affine:local:protein2protein]]] ** Message: 05:09:39.990: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.c ** Message: 05:09:41.461: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.c ** Message: 05:09:43.934: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] ** Message: 05:09:43.934: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o ** Message: 05:09:43.943: 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: 05:09:43.943: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 05:09:43.943: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 05:09:43.952: 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: 05:09:43.953: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.c ** Message: 05:09:44.264: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.c ** Message: 05:09:44.605: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.o] ** Message: 05:09:44.605: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.o ** Message: 05:09:44.614: Adding function [Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded] ** Message: 05:09:44.614: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.o] ** Message: 05:09:44.614: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.o ** Message: 05:09:44.623: Adding function [Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded] ** Message: 05:09:44.623: Processing model [a:o] ** Message: 05:09:44.624: Bootstrapper processing model [affine:overlap:dna2dna] ** Message: 05:09:44.624: Process optimal [optimal:affine:overlap:dna2dna] ** Message: 05:09:44.625: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.c ** Message: 05:09:45.275: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.c ** Message: 05:09:46.262: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.c ** Message: 05:09:47.231: 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_9/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.c ** Message: 05:09:48.025: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 05:09:49.138: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.o] ** Message: 05:09:49.138: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.o ** Message: 05:09:49.157: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score] ** Message: 05:09:49.158: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.o] ** Message: 05:09:49.158: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.o ** Message: 05:09:49.167: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path] ** Message: 05:09:49.167: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.o] ** Message: 05:09:49.167: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.o ** Message: 05:09:49.176: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region] ** Message: 05:09:49.177: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.o] ** Message: 05:09:49.177: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.o ** Message: 05:09:49.186: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint] ** Message: 05:09:49.187: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 05:09:49.187: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 05:09:49.196: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation] ** Message: 05:09:49.196: Processing model [e2g] ** Message: 05:09:49.197: Bootstrapper processing model [est2genome] ** Message: 05:09:49.197: Process optimal [optimal:est2genome] ** Message: 05:09:49.200: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_est2genome_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_est2genome_32_find_32_score.c ** Message: 05:09:50.027: 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_9/optimal_58_est2genome_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_est2genome_32_find_32_path.c ** Message: 05:09:51.213: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_est2genome_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_est2genome_32_find_32_region.c ** Message: 05:09:52.220: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_est2genome_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_est2genome_32_find_32_checkpoint.c ** Message: 05:09:55.099: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_est2genome_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_est2genome_32_find_32_path_32_continuation.c ** Message: 05:10:00.974: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_est2genome_32_find_32_score.o] ** Message: 05:10:00.974: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_est2genome_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_est2genome_32_find_32_score.o ** Message: 05:10:00.983: Adding function [optimal_58_est2genome_32_find_32_score] ** Message: 05:10:00.983: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_est2genome_32_find_32_path.o] ** Message: 05:10:00.983: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_est2genome_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_est2genome_32_find_32_path.o ** Message: 05:10:00.992: Adding function [optimal_58_est2genome_32_find_32_path] ** Message: 05:10:00.992: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_est2genome_32_find_32_region.o] ** Message: 05:10:00.992: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_est2genome_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_est2genome_32_find_32_region.o ** Message: 05:10:01.002: Adding function [optimal_58_est2genome_32_find_32_region] ** Message: 05:10:01.003: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_est2genome_32_find_32_checkpoint.o] ** Message: 05:10:01.003: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_est2genome_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_est2genome_32_find_32_checkpoint.o ** Message: 05:10:01.015: Adding function [optimal_58_est2genome_32_find_32_checkpoint] ** Message: 05:10:01.016: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_est2genome_32_find_32_path_32_continuation.o] ** Message: 05:10:01.016: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_est2genome_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_est2genome_32_find_32_path_32_continuation.o ** Message: 05:10:01.025: Adding function [optimal_58_est2genome_32_find_32_path_32_continuation] ** Message: 05:10:01.036: Process optimal [Terminal [Segment("START"->"match reverse"):[est2genome]]] ** Message: 05:10:01.040: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 05:10:02.413: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 05:10:05.101: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 05:10:05.102: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 05:10:05.118: 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: 05:10:05.118: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 05:10:05.118: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 05:10:05.126: 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: 05:10:05.126: Process optimal [Terminal [Segment("match reverse"->"END"):[est2genome]]] ** Message: 05:10:05.128: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 05:10:05.924: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 05:10:06.805: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 05:10:06.805: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 05:10:06.816: 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: 05:10:06.816: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 05:10:06.816: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 05:10:06.826: 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: 05:10:06.826: Process optimal [Terminal [Segment("START"->"match forward"):[est2genome]]] ** Message: 05:10:06.830: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 05:10:08.743: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 05:10:11.351: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 05:10:11.352: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 05:10:11.359: 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: 05:10:11.360: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 05:10:11.360: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 05:10:11.368: 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: 05:10:11.368: Process optimal [Terminal [Segment("match forward"->"END"):[est2genome]]] ** Message: 05:10:11.370: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 05:10:12.044: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 05:10:13.446: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 05:10:13.446: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 05:10:13.454: 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: 05:10:13.454: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 05:10:13.454: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 05:10:13.462: 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: 05:10:13.462: Process optimal [HeuristicJoin:[Segment("match reverse"->"match reverse"):[est2genome]]] ** Message: 05:10:13.467: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 05:10:16.672: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 05:10:20.715: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 05:10:20.715: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 05:10:20.725: 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: 05:10:20.726: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 05:10:20.726: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 05:10:20.736: 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: 05:10:20.737: Process optimal [Src span [Segment("match reverse"->"intron reverse"):[est2genome]]] ** Message: 05:10:20.739: 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_9/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 05:10:21.875: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 05:10:23.093: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 05:10:23.093: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 05:10:23.105: 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: 05:10:23.105: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 05:10:23.106: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 05:10:23.117: 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: 05:10:23.117: Process optimal [Src span traceback [Segment("match reverse"->"intron reverse"):[est2genome]]] ** Message: 05:10:23.123: 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_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 05:10:27.214: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 05:10:27.214: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 05:10:27.225: 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: 05:10:27.226: Process optimal [Dst span [Segment("intron reverse"->"match reverse"):[est2genome]]] ** Message: 05:10:27.229: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 05:10:29.302: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 05:10:32.201: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 05:10:32.201: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 05:10:32.212: 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: 05:10:32.213: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 05:10:32.213: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 05:10:32.224: 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: 05:10:32.224: Process optimal [HeuristicJoin:[Segment("match forward"->"match forward"):[est2genome]]] ** Message: 05:10:32.229: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 05:10:35.845: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 05:10:41.532: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 05:10:41.566: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 05:10:41.579: 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: 05:10:41.579: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 05:10:41.579: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 05:10:41.590: 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: 05:10:41.590: Process optimal [Src span [Segment("match forward"->"intron forward"):[est2genome]]] ** Message: 05:10:41.593: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 05:10:42.689: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 05:10:44.238: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 05:10:44.238: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 05:10:44.251: 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: 05:10:44.251: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 05:10:44.251: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 05:10:44.263: 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: 05:10:44.263: Process optimal [Src span traceback [Segment("match forward"->"intron forward"):[est2genome]]] ** Message: 05:10:44.269: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 05:10:49.143: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 05:10:49.144: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 05:10:49.154: 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: 05:10:49.155: Process optimal [Dst span [Segment("intron forward"->"match forward"):[est2genome]]] ** Message: 05:10:49.158: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 05:10:51.106: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 05:10:53.026: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 05:10:53.027: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 05:10:53.040: 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: 05:10:53.040: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 05:10:53.040: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 05:10:53.053: 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: 05:10:53.054: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.c ** Message: 05:10:53.644: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.c ** Message: 05:10:54.324: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.o] ** Message: 05:10:54.324: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.o ** Message: 05:10:54.336: Adding function [Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary] ** Message: 05:10:54.336: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.o] ** Message: 05:10:54.336: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.o ** Message: 05:10:54.349: Adding function [Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary] ** Message: 05:10:54.349: Processing model [ner] ** Message: 05:10:54.350: Bootstrapper processing model [NER:affine:local:dna2dna] ** Message: 05:10:54.350: Process optimal [optimal:NER:affine:local:dna2dna] ** Message: 05:10:54.351: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.c ** Message: 05:10:54.739: 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_9/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.c ** Message: 05:10:55.264: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.c ** Message: 05:10:55.683: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.c ** Message: 05:10:56.271: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 05:10:56.998: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.o] ** Message: 05:10:56.999: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.o ** Message: 05:10:57.007: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score] ** Message: 05:10:57.008: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.o] ** Message: 05:10:57.008: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.o ** Message: 05:10:57.021: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path] ** Message: 05:10:57.021: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.o] ** Message: 05:10:57.021: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.o ** Message: 05:10:57.033: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region] ** Message: 05:10:57.033: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o] ** Message: 05:10:57.033: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o ** Message: 05:10:57.045: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint] ** Message: 05:10:57.045: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 05:10:57.045: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 05:10:57.057: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation] ** Message: 05:10:57.064: Process optimal [Terminal [Segment("START"->"match"):[NER:affine:local:dna2dna]]] ** Message: 05:10:57.066: 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_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.c ** Message: 05:10:57.959: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.c ** Message: 05:10:59.496: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] ** Message: 05:10:59.497: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o ** Message: 05:10:59.508: 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: 05:10:59.508: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 05:10:59.508: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 05:10:59.517: 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: 05:10:59.517: Process optimal [Terminal [Segment("match"->"END"):[NER:affine:local:dna2dna]]] ** Message: 05:10:59.519: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.c ** Message: 05:10:59.924: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.c ** Message: 05:11:00.891: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] ** Message: 05:11:00.891: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o ** Message: 05:11:00.903: 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: 05:11:00.903: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 05:11:00.903: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 05:11:00.915: 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: 05:11:00.915: Process optimal [HeuristicJoin:[Segment("match"->"match"):[NER:affine:local:dna2dna]]] ** Message: 05:11:00.919: 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_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.c ** Message: 05:11:03.394: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.c ** Message: 05:11:07.195: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] ** Message: 05:11:07.196: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o ** Message: 05:11:07.205: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score] ** Message: 05:11:07.205: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 05:11:07.205: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 05:11:07.215: 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: 05:11:07.215: Process optimal [Src span [Segment("match"->"ner"):[NER:affine:local:dna2dna]]] ** Message: 05:11:07.217: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.c ** Message: 05:11:07.712: 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_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.c ** Message: 05:11:08.374: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] ** Message: 05:11:08.375: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o ** Message: 05:11:08.387: 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: 05:11:08.387: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 05:11:08.387: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 05:11:08.400: 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: 05:11:08.400: Process optimal [Src span traceback [Segment("match"->"ner"):[NER:affine:local:dna2dna]]] ** Message: 05:11:08.404: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.c ** Message: 05:11:11.423: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 05:11:11.423: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 05:11:11.435: 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: 05:11:11.435: Process optimal [Dst span [Segment("ner"->"match"):[NER:affine:local:dna2dna]]] ** Message: 05:11:11.437: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.c ** Message: 05:11:12.185: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.c ** Message: 05:11:13.751: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] ** Message: 05:11:13.751: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o ** Message: 05:11:13.799: 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: 05:11:13.800: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 05:11:13.800: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 05:11:13.814: 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: 05:11:13.815: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.c ** Message: 05:11:14.079: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.c ** Message: 05:11:14.421: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.o] ** Message: 05:11:14.421: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.o ** Message: 05:11:14.435: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary] ** Message: 05:11:14.436: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.o] ** Message: 05:11:14.436: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.o ** Message: 05:11:14.449: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary] ** Message: 05:11:14.450: Bootstrapper processing model [NER:affine:local:protein2protein] ** Message: 05:11:14.450: Process optimal [optimal:NER:affine:local:protein2protein] ** Message: 05:11:14.451: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.c ** Message: 05:11:14.740: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.c ** Message: 05:11:15.124: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.c ** Message: 05:11:15.647: 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_9/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.c ** Message: 05:11:16.274: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.c ** Message: 05:11:17.458: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.o] ** Message: 05:11:17.458: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.o ** Message: 05:11:17.468: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score] ** Message: 05:11:17.468: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.o] ** Message: 05:11:17.469: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.o ** Message: 05:11:17.479: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path] ** Message: 05:11:17.479: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.o] ** Message: 05:11:17.479: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.o ** Message: 05:11:17.489: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region] ** Message: 05:11:17.489: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o] ** Message: 05:11:17.491: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o ** Message: 05:11:17.502: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint] ** Message: 05:11:17.502: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o] ** Message: 05:11:17.503: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o ** Message: 05:11:17.515: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation] ** Message: 05:11:17.521: Process optimal [Terminal [Segment("START"->"match"):[NER:affine:local:protein2protein]]] ** Message: 05:11:17.523: 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_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.c ** Message: 05:11:18.256: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.c ** Message: 05:11:19.593: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] ** Message: 05:11:19.593: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o ** Message: 05:11:19.605: 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: 05:11:19.606: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 05:11:19.606: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 05:11:19.619: 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: 05:11:19.619: Process optimal [Terminal [Segment("match"->"END"):[NER:affine:local:protein2protein]]] ** Message: 05:11:19.622: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.c ** Message: 05:11:20.276: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.c ** Message: 05:11:21.309: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] ** Message: 05:11:21.309: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o ** Message: 05:11:21.325: 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: 05:11:21.325: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 05:11:21.325: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 05:11:21.341: 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: 05:11:21.341: Process optimal [HeuristicJoin:[Segment("match"->"match"):[NER:affine:local:protein2protein]]] ** Message: 05:11:21.345: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.c ** Message: 05:11:23.638: 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_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.c ** Message: 05:11:27.263: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] ** Message: 05:11:27.263: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o ** Message: 05:11:27.274: 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: 05:11:27.274: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 05:11:27.274: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 05:11:27.284: 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: 05:11:27.284: Process optimal [Src span [Segment("match"->"ner"):[NER:affine:local:protein2protein]]] ** Message: 05:11:27.285: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.c ** Message: 05:11:27.713: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.c ** Message: 05:11:28.727: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] ** Message: 05:11:28.727: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o ** Message: 05:11:28.738: 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: 05:11:28.738: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 05:11:28.739: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 05:11:28.749: 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: 05:11:28.749: Process optimal [Src span traceback [Segment("match"->"ner"):[NER:affine:local:protein2protein]]] ** Message: 05:11:28.752: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.c ** Message: 05:11:31.501: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 05:11:31.501: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 05:11:31.512: 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: 05:11:31.512: Process optimal [Dst span [Segment("ner"->"match"):[NER:affine:local:protein2protein]]] ** Message: 05:11:31.514: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.c ** Message: 05:11:32.099: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.c ** Message: 05:11:33.025: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] ** Message: 05:11:33.026: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o ** Message: 05:11:33.036: 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: 05:11:33.036: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 05:11:33.037: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 05:11:33.047: 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: 05:11:33.048: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.c ** Message: 05:11:33.276: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.c ** Message: 05:11:33.592: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.o] ** Message: 05:11:33.600: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.o ** Message: 05:11:33.622: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary] ** Message: 05:11:33.622: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.o] ** Message: 05:11:33.622: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.o ** Message: 05:11:33.635: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary] ** Message: 05:11:33.635: Processing model [p2d] ** Message: 05:11:33.635: Bootstrapper processing model [protein2dna:local] ** Message: 05:11:33.635: Process optimal [optimal:protein2dna:local] ** Message: 05:11:33.637: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_local_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_local_32_find_32_score.c ** Message: 05:11:33.999: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_local_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_local_32_find_32_path.c ** Message: 05:11:34.637: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_local_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_local_32_find_32_region.c ** Message: 05:11:35.147: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_local_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_local_32_find_32_checkpoint.c ** Message: 05:11:36.469: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.c ** Message: 05:11:38.444: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_local_32_find_32_score.o] ** Message: 05:11:38.444: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_local_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_local_32_find_32_score.o ** Message: 05:11:38.455: Adding function [optimal_58_protein2dna_58_local_32_find_32_score] ** Message: 05:11:38.455: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_local_32_find_32_path.o] ** Message: 05:11:38.455: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_local_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_local_32_find_32_path.o ** Message: 05:11:38.466: Adding function [optimal_58_protein2dna_58_local_32_find_32_path] ** Message: 05:11:38.466: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_local_32_find_32_region.o] ** Message: 05:11:38.467: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_local_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_local_32_find_32_region.o ** Message: 05:11:38.477: Adding function [optimal_58_protein2dna_58_local_32_find_32_region] ** Message: 05:11:38.478: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_local_32_find_32_checkpoint.o] ** Message: 05:11:38.478: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_local_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_local_32_find_32_checkpoint.o ** Message: 05:11:38.488: Adding function [optimal_58_protein2dna_58_local_32_find_32_checkpoint] ** Message: 05:11:38.488: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.o] ** Message: 05:11:38.488: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.o ** Message: 05:11:38.498: Adding function [optimal_58_protein2dna_58_local_32_find_32_path_32_continuation] ** Message: 05:11:38.505: Process optimal [Terminal [Segment("START"->"match"):[protein2dna:local]]] ** Message: 05:11:38.507: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.c ** Message: 05:11:40.007: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.c ** Message: 05:11:42.969: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] ** Message: 05:11:42.969: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o ** Message: 05:11:42.980: 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: 05:11:42.980: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] ** Message: 05:11:42.981: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o ** Message: 05:11:42.992: 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: 05:11:42.992: Process optimal [Terminal [Segment("match"->"END"):[protein2dna:local]]] ** Message: 05:11:42.994: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.c ** Message: 05:11:43.567: 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_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.c ** Message: 05:11:44.844: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] ** Message: 05:11:44.844: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o ** Message: 05:11:44.856: 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: 05:11:44.856: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] ** Message: 05:11:44.856: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o ** Message: 05:11:44.867: 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: 05:11:44.867: Process optimal [HeuristicJoin:[Segment("match"->"match"):[protein2dna:local]]] ** Message: 05:11:44.870: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.c ** Message: 05:11:47.986: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.c ** Message: 05:11:53.810: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] ** Message: 05:11:53.810: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o ** Message: 05:11:53.825: 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: 05:11:53.825: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] ** Message: 05:11:53.826: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o ** Message: 05:11:53.841: 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: 05:11:53.842: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.c ** Message: 05:11:54.181: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.c ** Message: 05:11:54.566: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.o] ** Message: 05:11:54.566: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.o ** Message: 05:11:54.582: Adding function [Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded] ** Message: 05:11:54.582: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.o] ** Message: 05:11:54.583: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.o ** Message: 05:11:54.598: Adding function [Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded] ** Message: 05:11:54.599: Processing model [p2d:b] ** Message: 05:11:54.599: Bootstrapper processing model [protein2dna:bestfit] ** Message: 05:11:54.599: Process optimal [optimal:protein2dna:bestfit] ** Message: 05:11:54.603: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_bestfit_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_bestfit_32_find_32_score.c ** Message: 05:11:56.916: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_bestfit_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_bestfit_32_find_32_path.c ** Message: 05:12:00.182: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_bestfit_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_bestfit_32_find_32_region.c ** Message: 05:12:02.992: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.c ** Message: 05:12:04.250: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.c ** Message: 05:12:05.903: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_bestfit_32_find_32_score.o] ** Message: 05:12:05.903: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_bestfit_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_bestfit_32_find_32_score.o ** Message: 05:12:05.919: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_score] ** Message: 05:12:05.919: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_bestfit_32_find_32_path.o] ** Message: 05:12:05.919: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_bestfit_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_bestfit_32_find_32_path.o ** Message: 05:12:05.934: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_path] ** Message: 05:12:05.935: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_bestfit_32_find_32_region.o] ** Message: 05:12:05.935: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_bestfit_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_bestfit_32_find_32_region.o ** Message: 05:12:05.952: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_region] ** Message: 05:12:05.953: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.o] ** Message: 05:12:05.953: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.o ** Message: 05:12:05.968: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint] ** Message: 05:12:05.968: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.o] ** Message: 05:12:05.969: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.o ** Message: 05:12:05.985: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation] ** Message: 05:12:05.986: Processing model [p2g] ** Message: 05:12:05.987: Bootstrapper processing model [protein2genome:local] ** Message: 05:12:05.987: Process optimal [optimal:protein2genome:local] ** Message: 05:12:05.990: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_local_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_local_32_find_32_score.c ** Message: 05:12:07.269: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_local_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_local_32_find_32_path.c ** Message: 05:12:09.340: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_local_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_local_32_find_32_region.c ** Message: 05:12:11.420: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_local_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_local_32_find_32_checkpoint.c ** Message: 05:12:20.322: 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_9/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.c ** Message: 05:12:30.063: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_local_32_find_32_score.o] ** Message: 05:12:30.063: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_local_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_local_32_find_32_score.o ** Message: 05:12:30.078: Adding function [optimal_58_protein2genome_58_local_32_find_32_score] ** Message: 05:12:30.078: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_local_32_find_32_path.o] ** Message: 05:12:30.078: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_local_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_local_32_find_32_path.o ** Message: 05:12:30.093: Adding function [optimal_58_protein2genome_58_local_32_find_32_path] ** Message: 05:12:30.093: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_local_32_find_32_region.o] ** Message: 05:12:30.093: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_local_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_local_32_find_32_region.o ** Message: 05:12:30.108: Adding function [optimal_58_protein2genome_58_local_32_find_32_region] ** Message: 05:12:30.109: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_local_32_find_32_checkpoint.o] ** Message: 05:12:30.109: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_local_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_local_32_find_32_checkpoint.o ** Message: 05:12:30.121: Adding function [optimal_58_protein2genome_58_local_32_find_32_checkpoint] ** Message: 05:12:30.121: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.o] ** Message: 05:12:30.121: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.o ** Message: 05:12:30.138: Adding function [optimal_58_protein2genome_58_local_32_find_32_path_32_continuation] ** Message: 05:12:30.163: Process optimal [Terminal [Segment("START"->"match"):[protein2genome:local]]] ** Message: 05:12:30.168: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 05:12:37.999: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 05:12:48.168: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 05:12:48.168: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 05:12:48.189: 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: 05:12:48.189: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 05:12:48.189: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 05:12:48.206: 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: 05:12:48.206: Process optimal [Terminal [Segment("match"->"END"):[protein2genome:local]]] ** Message: 05:12:48.211: 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_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 05:12:51.404: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 05:12:56.710: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 05:12:56.711: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 05:12:56.727: 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: 05:12:56.727: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 05:12:56.727: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 05:12:56.745: 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: 05:12:56.745: Process optimal [HeuristicJoin:[Segment("match"->"match"):[protein2genome:local]]] ** Message: 05:12:56.758: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 05:13:13.465: 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_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 05:13:38.524: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 05:13:38.525: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 05:13:38.543: 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: 05:13:38.543: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 05:13:38.543: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 05:13:38.569: 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: 05:13:38.569: Process optimal [Src span [Segment("match"->"intron 0:0 phase-T"):[protein2genome:local]]] ** Message: 05:13:38.573: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 05:13:41.811: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 05:13:47.425: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 05:13:47.425: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 05:13:47.439: 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: 05:13:47.439: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 05:13:47.439: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 05:13:47.452: 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: 05:13:47.453: Process optimal [Src span traceback [Segment("match"->"intron 0:0 phase-T"):[protein2genome:local]]] ** Message: 05:13:47.461: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 05:14:18.137: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 05:14:18.138: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 05:14:18.156: 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: 05:14:18.156: Process optimal [Dst span [Segment("intron 0:0 phase-T"->"match"):[protein2genome:local]]] ** Message: 05:14:18.164: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 05:14:25.494: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 05:14:38.783: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 05:14:38.783: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 05:14:38.801: 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: 05:14:38.801: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 05:14:38.801: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 05:14:38.820: 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: 05:14:38.820: Process optimal [Src span [Segment("match"->"intron 1:2 phase-T"):[protein2genome:local]]] ** Message: 05:14:38.825: 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_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 05:14:42.908: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 05:14:50.276: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 05:14:50.276: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 05:14:50.295: 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: 05:14:50.295: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 05:14:50.295: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 05:14:50.315: 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: 05:14:50.315: Process optimal [Src span traceback [Segment("match"->"intron 1:2 phase-T"):[protein2genome:local]]] ** Message: 05:14:50.330: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 05:15:14.276: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 05:15:14.276: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 05:15:14.292: 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: 05:15:14.292: Process optimal [Dst span [Segment("intron 1:2 phase-T"->"match"):[protein2genome:local]]] ** Message: 05:15:14.298: 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_9/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 05:15:21.566: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 05:15:36.209: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 05:15:36.209: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 05:15:36.230: 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: 05:15:36.230: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 05:15:36.230: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 05:15:36.249: 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: 05:15:36.250: Process optimal [Src span [Segment("match"->"intron 2:1 phase-T"):[protein2genome:local]]] ** Message: 05:15:36.255: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 05:15:39.794: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 05:15:45.444: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 05:15:45.444: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 05:15:45.463: 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: 05:15:45.463: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 05:15:45.463: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 05:15:45.482: 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: 05:15:45.482: Process optimal [Src span traceback [Segment("match"->"intron 2:1 phase-T"):[protein2genome:local]]] ** Message: 05:15:45.496: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 05:16:12.238: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 05:16:12.239: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 05:16:12.258: 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: 05:16:12.259: Process optimal [Dst span [Segment("intron 2:1 phase-T"->"match"):[protein2genome:local]]] ** Message: 05:16:12.267: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 05:16:18.577: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 05:16:37.844: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 05:16:37.844: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 05:16:37.874: 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: 05:16:37.874: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 05:16:37.874: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 05:16:37.904: 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: 05:16:37.906: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.c ** Message: 05:16:39.877: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.c ** Message: 05:16:41.972: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.o] ** Message: 05:16:41.972: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.o ** Message: 05:16:41.992: Adding function [Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary] ** Message: 05:16:41.992: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.o] ** Message: 05:16:41.993: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.o ** Message: 05:16:42.022: Adding function [Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary] ** Message: 05:16:42.023: Processing model [p2g:b] ** Message: 05:16:42.025: Bootstrapper processing model [protein2genome:bestfit] ** Message: 05:16:42.025: Process optimal [optimal:protein2genome:bestfit] ** Message: 05:16:42.035: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_bestfit_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_bestfit_32_find_32_score.c ** Message: 05:16:58.494: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_bestfit_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_bestfit_32_find_32_path.c ** Message: 05:17:20.637: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_bestfit_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_bestfit_32_find_32_region.c ** Message: 05:17:34.345: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.c ** Message: 05:17:42.855: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.c ** Message: 05:17:55.184: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_bestfit_32_find_32_score.o] ** Message: 05:17:55.184: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_bestfit_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_bestfit_32_find_32_score.o ** Message: 05:17:55.204: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_score] ** Message: 05:17:55.204: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_bestfit_32_find_32_path.o] ** Message: 05:17:55.204: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_bestfit_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_bestfit_32_find_32_path.o ** Message: 05:17:55.224: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_path] ** Message: 05:17:55.225: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_bestfit_32_find_32_region.o] ** Message: 05:17:55.225: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_bestfit_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_bestfit_32_find_32_region.o ** Message: 05:17:55.245: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_region] ** Message: 05:17:55.245: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.o] ** Message: 05:17:55.245: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.o ** Message: 05:17:55.266: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint] ** Message: 05:17:55.266: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.o] ** Message: 05:17:55.266: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.o ** Message: 05:17:55.286: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation] ** Message: 05:17:55.287: Processing model [c2c] ** Message: 05:17:55.288: Bootstrapper processing model [coding2coding] ** Message: 05:17:55.288: Process optimal [optimal:coding2coding] ** Message: 05:17:55.291: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2coding_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2coding_32_find_32_score.c ** Message: 05:17:57.090: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2coding_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2coding_32_find_32_path.c ** Message: 05:18:01.081: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2coding_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2coding_32_find_32_region.c ** Message: 05:18:04.158: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2coding_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2coding_32_find_32_checkpoint.c ** Message: 05:18:14.366: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2coding_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2coding_32_find_32_path_32_continuation.c ** Message: 05:18:25.709: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2coding_32_find_32_score.o] ** Message: 05:18:25.709: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2coding_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2coding_32_find_32_score.o ** Message: 05:18:25.730: Adding function [optimal_58_coding2coding_32_find_32_score] ** Message: 05:18:25.730: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2coding_32_find_32_path.o] ** Message: 05:18:25.730: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2coding_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2coding_32_find_32_path.o ** Message: 05:18:25.750: Adding function [optimal_58_coding2coding_32_find_32_path] ** Message: 05:18:25.751: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2coding_32_find_32_region.o] ** Message: 05:18:25.751: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2coding_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2coding_32_find_32_region.o ** Message: 05:18:25.772: Adding function [optimal_58_coding2coding_32_find_32_region] ** Message: 05:18:25.772: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2coding_32_find_32_checkpoint.o] ** Message: 05:18:25.772: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2coding_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2coding_32_find_32_checkpoint.o ** Message: 05:18:25.793: Adding function [optimal_58_coding2coding_32_find_32_checkpoint] ** Message: 05:18:25.793: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2coding_32_find_32_path_32_continuation.o] ** Message: 05:18:25.793: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2coding_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2coding_32_find_32_path_32_continuation.o ** Message: 05:18:25.813: Adding function [optimal_58_coding2coding_32_find_32_path_32_continuation] ** Message: 05:18:25.848: Process optimal [Terminal [Segment("START"->"match"):[coding2coding]]] ** Message: 05:18:25.855: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.c ** Message: 05:18:32.301: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.c ** Message: 05:18:46.015: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o] ** Message: 05:18:46.016: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o ** Message: 05:18:46.038: 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: 05:18:46.038: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o] ** Message: 05:18:46.038: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o ** Message: 05:18:46.061: 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: 05:18:46.061: Process optimal [Terminal [Segment("match"->"END"):[coding2coding]]] ** Message: 05:18:46.075: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_score.c ** Message: 05:18:48.666: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_path.c ** Message: 05:18:53.117: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_score.o] ** Message: 05:18:53.168: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_score.o ** Message: 05:18:53.189: 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: 05:18:53.190: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_path.o] ** Message: 05:18:53.190: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_path.o ** Message: 05:18:53.208: 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: 05:18:53.208: Process optimal [HeuristicJoin:[Segment("match"->"match"):[coding2coding]]] ** Message: 05:18:53.216: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.c ** Message: 05:19:06.192: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.c ** Message: 05:19:40.215: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o] ** Message: 05:19:40.216: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o ** Message: 05:19:40.235: 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: 05:19:40.235: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o] ** Message: 05:19:40.235: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o ** Message: 05:19:40.255: 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: 05:19:40.256: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.c ** Message: 05:19:41.097: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.c ** Message: 05:19:41.646: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.o] ** Message: 05:19:41.647: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.o ** Message: 05:19:41.670: Adding function [Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded] ** Message: 05:19:41.670: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.o] ** Message: 05:19:41.670: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.o ** Message: 05:19:41.693: Adding function [Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded] ** Message: 05:19:41.693: Processing model [c2g] ** Message: 05:19:41.695: Bootstrapper processing model [coding2genome] ** Message: 05:19:41.695: Process optimal [optimal:coding2genome] ** Message: 05:19:41.701: 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_9/optimal_58_coding2genome_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2genome_32_find_32_score.c ** Message: 05:19:45.850: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2genome_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2genome_32_find_32_path.c ** Message: 05:19:52.617: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2genome_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2genome_32_find_32_region.c ** Message: 05:19:59.319: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2genome_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2genome_32_find_32_checkpoint.c ** Message: 05:20:17.328: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2genome_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2genome_32_find_32_path_32_continuation.c ** Message: 05:20:44.238: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2genome_32_find_32_score.o] ** Message: 05:20:44.238: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2genome_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2genome_32_find_32_score.o ** Message: 05:20:44.261: Adding function [optimal_58_coding2genome_32_find_32_score] ** Message: 05:20:44.261: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2genome_32_find_32_path.o] ** Message: 05:20:44.261: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2genome_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2genome_32_find_32_path.o ** Message: 05:20:44.285: Adding function [optimal_58_coding2genome_32_find_32_path] ** Message: 05:20:44.285: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2genome_32_find_32_region.o] ** Message: 05:20:44.285: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2genome_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2genome_32_find_32_region.o ** Message: 05:20:44.307: Adding function [optimal_58_coding2genome_32_find_32_region] ** Message: 05:20:44.308: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2genome_32_find_32_checkpoint.o] ** Message: 05:20:44.308: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2genome_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2genome_32_find_32_checkpoint.o ** Message: 05:20:44.331: Adding function [optimal_58_coding2genome_32_find_32_checkpoint] ** Message: 05:20:44.331: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2genome_32_find_32_path_32_continuation.o] ** Message: 05:20:44.332: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2genome_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_coding2genome_32_find_32_path_32_continuation.o ** Message: 05:20:44.355: Adding function [optimal_58_coding2genome_32_find_32_path_32_continuation] ** Message: 05:20:44.356: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.c ** Message: 05:20:44.861: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.c ** Message: 05:20:45.523: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.o] ** Message: 05:20:45.524: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.o ** Message: 05:20:45.541: Adding function [Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary] ** Message: 05:20:45.541: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.o] ** Message: 05:20:45.542: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.o ** Message: 05:20:45.564: Adding function [Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary] ** Message: 05:20:45.564: Processing model [cd2g] ** Message: 05:20:45.567: Bootstrapper processing model [cdna2genome] ** Message: 05:20:45.567: Process optimal [optimal:cdna2genome] ** Message: 05:20:45.577: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_cdna2genome_32_find_32_score.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_cdna2genome_32_find_32_score.c ** Message: 05:20:57.231: 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_9/optimal_58_cdna2genome_32_find_32_path.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_cdna2genome_32_find_32_path.c ** Message: 05:21:16.066: 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_9/optimal_58_cdna2genome_32_find_32_region.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_cdna2genome_32_find_32_region.c ** Message: 05:21:31.487: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_cdna2genome_32_find_32_checkpoint.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_cdna2genome_32_find_32_checkpoint.c ** Message: 05:23:36.414: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_cdna2genome_32_find_32_path_32_continuation.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_cdna2genome_32_find_32_path_32_continuation.c ** Message: 05:26:18.612: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_cdna2genome_32_find_32_score.o] ** Message: 05:26:18.612: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_cdna2genome_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_cdna2genome_32_find_32_score.o ** Message: 05:26:18.635: Adding function [optimal_58_cdna2genome_32_find_32_score] ** Message: 05:26:18.635: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_cdna2genome_32_find_32_path.o] ** Message: 05:26:18.635: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_cdna2genome_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_cdna2genome_32_find_32_path.o ** Message: 05:26:18.659: Adding function [optimal_58_cdna2genome_32_find_32_path] ** Message: 05:26:18.659: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_cdna2genome_32_find_32_region.o] ** Message: 05:26:18.660: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_cdna2genome_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_cdna2genome_32_find_32_region.o ** Message: 05:26:18.685: Adding function [optimal_58_cdna2genome_32_find_32_region] ** Message: 05:26:18.685: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_cdna2genome_32_find_32_checkpoint.o] ** Message: 05:26:18.685: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_cdna2genome_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_cdna2genome_32_find_32_checkpoint.o ** Message: 05:26:18.709: Adding function [optimal_58_cdna2genome_32_find_32_checkpoint] ** Message: 05:26:18.709: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_cdna2genome_32_find_32_path_32_continuation.o] ** Message: 05:26:18.709: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_cdna2genome_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/optimal_58_cdna2genome_32_find_32_path_32_continuation.o ** Message: 05:26:18.732: Adding function [optimal_58_cdna2genome_32_find_32_path_32_continuation] ** Message: 05:26:18.734: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.c ** Message: 05:26:19.777: Compiling codegen: cc -pipe -O2 -fno-strict-aliasing -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/struct -I/construction/biology/exonerate/exonerate-2.4.0/src/general -I/construction/biology/exonerate/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/construction/biology/exonerate/exonerate-2.4.0/src/model -I/construction/biology/exonerate/exonerate-2.4.0/src/comparison -I/construction/biology/exonerate/exonerate-2.4.0/src/c4 -I/construction/biology/exonerate/exonerate-2.4.0/src/bsdp -I/construction/biology/exonerate/exonerate-2.4.0/src/sdp -o /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o -c /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.c ** Message: 05:26:21.201: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o] ** Message: 05:26:21.212: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o ** Message: 05:26:21.237: Adding function [Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary] ** Message: 05:26:21.237: Adding: [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o] ** Message: 05:26:21.238: Adding object file [/construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /construction/biology/exonerate/exonerate-2.4.0/codegen/x86_64_45_portbld_45_dragonfly5_46_9/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o ** Message: 05:26:21.266: Adding function [Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary] ** Message: 05:26:21.267: 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: 05:26:21.591: Adding: [c4_model_lookup.o] ** Message: 05:26:21.591: Adding object file [c4_model_lookup.o] to archive ar -Sq c4_model_archive.a c4_model_lookup.o ** Message: 05:26:21.613: Indexing archive [c4_model_archive.a] ranlib c4_model_archive.a ** Message: 05:26:21.665: Done ** Message: 05:26:21.665: Finished building bootstrapping components cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/hub -I../../src/general -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I. -DUSE_COMPILED_MODELS -c ../../src/c4/viterbi.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/hub -I../../src/general -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I. -DUSE_COMPILED_MODELS -c ../../src/sdp/scheduler.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o exonerate exonerate.o viterbi.o scheduler.o c4_model_archive.a ../../src/comparison/wordhood.o ../../src/comparison/hspset.o ../../src/comparison/seeder.o ../../src/comparison/comparison.o ../../src/database/fastapipe.o ../../src/database/fastadb.o ../../src/struct/dejavu.o ../../src/struct/fsm.o ../../src/struct/vfsm.o ../../src/struct/sparsecache.o ../../src/hub/gam.o ../../src/hub/bsam.o ../../src/hub/analysis.o ../../src/general/compoundfile.o ../../src/general/threadref.o ../../src/c4/c4.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/opair.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/layout.o ../../src/c4/region.o ../../src/c4/subopt.o ../../src/bsdp/bsdp.o ../../src/bsdp/sar.o ../../src/bsdp/heuristic.o ../../src/bsdp/hpair.o ../../src/sdp/boundary.o ../../src/sdp/sdp.o ../../src/sdp/lookahead.o ../../src/sdp/straceback.o ../../src/struct/matrix.o ../../src/struct/slist.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/translate.o ../../src/sequence/splice.o ../../src/model/affine.o ../../src/model/est2genome.o ../../src/model/ner.o ../../src/model/protein2dna.o ../../src/model/protein2genome.o ../../src/model/coding2coding.o ../../src/model/coding2genome.o ../../src/model/cdna2genome.o ../../src/model/genome2genome.o ../../src/model/ungapped.o ../../src/model/intron.o ../../src/model/frameshift.o ../../src/model/phase.o ../../src/model/modeltype.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/socket.o ../../src/general/jobqueue.o ../../src/comparison/match.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/hub -I../../src/general -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c ipcress.c ipcress.c: In function 'Ipcress_prepare_PCR': ipcress.c:264:9: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] g_strup(primer_a); ^~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:82, from ipcress.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here gchar* g_strup (gchar *string); ^~~~~~~ ipcress.c:265:9: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] g_strup(primer_b); ^~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:82, from ipcress.c:16: /usr/local/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here gchar* g_strup (gchar *string); ^~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o ipcress ipcress.o ../../src/comparison/pcr.o ../../src/comparison/wordhood.o ../../src/database/fastadb.o ../../src/sequence/alphabet.o ../../src/sequence/sequence.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/struct/fsm.o ../../src/struct/slist.o ../../src/struct/matrix.o ../../src/struct/recyclebin.o ../../src/struct/sparsecache.o ../../src/general/lineparse.o ../../src/general/argument.o ../../src/general/compoundfile.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/hub -I../../src/general -DHOSTTYPE="\"x86_64-portbld-dragonfly5.9\"" -DSOURCE_ROOT_DIR="\"/construction/biology/exonerate/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c exonerate-server.c exonerate-server.c: In function 'Exonerate_Server_get_hsps': exonerate-server.c:349:13: warning: Deprecated pre-processor symbol, replace with g_string_sprintfa(str, "hspset: %d", index_hsp_set->target_id); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ exonerate-server.c:354:13: warning: Deprecated pre-processor symbol, replace with g_string_sprintfa(str, " %d %d %d", ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ exonerate-server.c:357:13: warning: Deprecated pre-processor symbol, replace with g_string_sprintfa(str, "\n"); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o exonerate-server exonerate-server.o ../../src/general/socket.o ../../src/general/argument.o ../../src/comparison/hspset.o ../../src/comparison/match.o ../../src/comparison/wordhood.o ../../src/database/dataset.o ../../src/database/index.o ../../src/database/fastadb.o ../../src/struct/bitarray.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/struct/splaytree.o ../../src/struct/noitree.o ../../src/struct/vfsm.o ../../src/struct/pqueue.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/translate.o ../../src/sequence/splice.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -L/usr/local/lib -lglib-2.0 -lintl Making all in util cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastaclean.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastaclean fastaclean.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastaclip.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastaclip fastaclip.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastachecksum.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastachecksum fastachecksum.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastacomposition.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastacomposition fastacomposition.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastadiff.c fastadiff.c: In function 'fasta_diff': fastadiff.c:70:13: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] comp = g_strcasecmp; ^~~~ In file included from /usr/local/include/glib-2.0/glib.h:82, from ../../src/general/argument.h:26, from fastadiff.c:19: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastadiff fastadiff.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastaexplode.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastaexplode fastaexplode.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastafetch.c fastafetch.c: In function 'get_query_list': fastafetch.c:121:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(query, "stdin")){ ^~ In file included from /usr/local/include/glib-2.0/glib.h:82, from ../../src/general/argument.h:26, from fastafetch.c:21: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastafetch fastafetch.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastahardmask.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastahardmask fastahardmask.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastaindex.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastaindex fastaindex.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastalength.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastalength fastalength.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastanrdb.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastanrdb fastanrdb.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastaoverlap.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastaoverlap fastaoverlap.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastareformat.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastareformat fastareformat.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastaremove.c fastaremove.c: In function 'Argument_main': fastaremove.c:73:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(remove_path, "stdin")){ ^~ In file included from /usr/local/include/glib-2.0/glib.h:82, from ../../src/general/argument.h:26, from fastaremove.c:19: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastaremove fastaremove.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastarevcomp.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastarevcomp fastarevcomp.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastasoftmask.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastasoftmask fastasoftmask.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastasort.c fastasort.c: In function 'SortKey_Mask_create': fastasort.c:130:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(sort_key, "id")) ^~ In file included from /usr/local/include/glib-2.0/glib.h:82, from ../../src/general/argument.h:26, from fastasort.c:20: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ fastasort.c:132:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] else if(!g_strcasecmp(sort_key, "len")) ^~~~ In file included from /usr/local/include/glib-2.0/glib.h:82, from ../../src/general/argument.h:26, from fastasort.c:20: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ fastasort.c:134:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] else if(!g_strcasecmp(sort_key, "seq")) ^~~~ In file included from /usr/local/include/glib-2.0/glib.h:82, from ../../src/general/argument.h:26, from fastasort.c:20: /usr/local/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastasort fastasort.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastasplit.c fastasplit.c: In function 'Argument_main': fastasplit.c:92:13: warning: 'g_basename' is deprecated: Use 'g_path_get_basename' instead [-Wdeprecated-declarations] output_dir, G_DIR_SEPARATOR, g_basename(query_path)); ^~~~~~~~~~ In file included from /usr/local/include/glib-2.0/glib.h:48, from ../../src/general/argument.h:26, from fastasplit.c:20: /usr/local/include/glib-2.0/glib/gfileutils.h:205:14: note: declared here const gchar *g_basename (const gchar *file_name); ^~~~~~~~~~ cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastasplit fastasplit.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastasubseq.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastasubseq fastasubseq.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastatranslate.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastatranslate fastatranslate.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastavalidcds.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastavalidcds fastavalidcds.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fasta2esd.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fasta2esd fasta2esd.o ../../src/database/dataset.o ../../src/struct/bitarray.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fastaannotatecdna.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o fastaannotatecdna fastaannotatecdna.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c esd2esi.c cc -pipe -O2 -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -L/usr/local/lib -lgthread-2.0 -pthread -lglib-2.0 -lintl -lpthread -o esd2esi esd2esi.o ../../src/database/dataset.o ../../src/database/index.o ../../src/general/threadref.o ../../src/struct/bitarray.o ../../src/struct/vfsm.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/struct/noitree.o ../../src/struct/splaytree.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/comparison/wordhood.o ../../src/comparison/hspset.o ../../src/comparison/match.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -L/usr/local/lib -lglib-2.0 -lintl Making all in test Making all in data Making all in cdna Making all in protein Making all in exonerate Making all in ipcress Making all in util SUCCEEDED 00:18:10 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for exonerate-2.4.0 ===> Generating temporary packing list Making install in doc Making install in man Making install in man1 /usr/bin/make install-man1 /bin/sh ../../../mkinstalldirs /construction/biology/exonerate/stage/usr/local/man/man1 install -m 0644 ./exonerate.1 /construction/biology/exonerate/stage/usr/local/man/man1/exonerate.1 install -m 0644 ./ipcress.1 /construction/biology/exonerate/stage/usr/local/man/man1/ipcress.1 install -m 0644 ./exonerate-server.1 /construction/biology/exonerate/stage/usr/local/man/man1/exonerate-server.1 install -m 0644 ./fastautils.1 /construction/biology/exonerate/stage/usr/local/man/man1/fastautils.1 Making install in src Making install in struct Making install in general Making install in sequence Making install in comparison Making install in database Making install in c4 Making install in bsdp Making install in sdp Making install in model Making install in hub Making install in program /bin/sh ../../mkinstalldirs /construction/biology/exonerate/stage/usr/local/bin install -s -m 555 exonerate /construction/biology/exonerate/stage/usr/local/bin/exonerate install -s -m 555 ipcress /construction/biology/exonerate/stage/usr/local/bin/ipcress install -s -m 555 exonerate-server /construction/biology/exonerate/stage/usr/local/bin/exonerate-server Making install in util /bin/sh ../../mkinstalldirs /construction/biology/exonerate/stage/usr/local/bin install -s -m 555 fastaclean /construction/biology/exonerate/stage/usr/local/bin/fastaclean install -s -m 555 fastaclip /construction/biology/exonerate/stage/usr/local/bin/fastaclip install -s -m 555 fastachecksum /construction/biology/exonerate/stage/usr/local/bin/fastachecksum install -s -m 555 fastacomposition /construction/biology/exonerate/stage/usr/local/bin/fastacomposition install -s -m 555 fastadiff /construction/biology/exonerate/stage/usr/local/bin/fastadiff install -s -m 555 fastaexplode /construction/biology/exonerate/stage/usr/local/bin/fastaexplode install -s -m 555 fastafetch /construction/biology/exonerate/stage/usr/local/bin/fastafetch install -s -m 555 fastahardmask /construction/biology/exonerate/stage/usr/local/bin/fastahardmask install -s -m 555 fastaindex /construction/biology/exonerate/stage/usr/local/bin/fastaindex install -s -m 555 fastalength /construction/biology/exonerate/stage/usr/local/bin/fastalength install -s -m 555 fastanrdb /construction/biology/exonerate/stage/usr/local/bin/fastanrdb install -s -m 555 fastaoverlap /construction/biology/exonerate/stage/usr/local/bin/fastaoverlap install -s -m 555 fastareformat /construction/biology/exonerate/stage/usr/local/bin/fastareformat install -s -m 555 fastaremove /construction/biology/exonerate/stage/usr/local/bin/fastaremove install -s -m 555 fastarevcomp /construction/biology/exonerate/stage/usr/local/bin/fastarevcomp install -s -m 555 fastasoftmask /construction/biology/exonerate/stage/usr/local/bin/fastasoftmask install -s -m 555 fastasort /construction/biology/exonerate/stage/usr/local/bin/fastasort install -s -m 555 fastasplit /construction/biology/exonerate/stage/usr/local/bin/fastasplit install -s -m 555 fastasubseq /construction/biology/exonerate/stage/usr/local/bin/fastasubseq install -s -m 555 fastatranslate /construction/biology/exonerate/stage/usr/local/bin/fastatranslate install -s -m 555 fastavalidcds /construction/biology/exonerate/stage/usr/local/bin/fastavalidcds install -s -m 555 fasta2esd /construction/biology/exonerate/stage/usr/local/bin/fasta2esd install -s -m 555 fastaannotatecdna /construction/biology/exonerate/stage/usr/local/bin/fastaannotatecdna install -s -m 555 esd2esi /construction/biology/exonerate/stage/usr/local/bin/esd2esi Making install in test Making install in data Making install in cdna Making install in protein Making install in exonerate Making install in ipcress Making install in util ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:02 ------------------------------------------------------------------------------- -- Phase: check-plist ------------------------------------------------------------------------------- ====> Checking for pkg-plist issues (check-plist) ===> Parsing plist ===> Checking for items in STAGEDIR missing from pkg-plist ===> Checking for items in pkg-plist which are not in STAGEDIR ===> No pkg-plist issues found (check-plist) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for exonerate-2.4.0 file sizes/checksums [31]: 0% file sizes/checksums [31]: 100% packing files [31]: 0% packing files [31]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:06 TOTAL TIME 00:18:31