=>> Building biology/exonerate build started at Thu Dec 11 14:30:37 EST 2025 port directory: /usr/ports/biology/exonerate package name: exonerate-2.4.0_1 building for: FreeBSD pkg.DaveG.ca 13.5-RELEASE-p7 FreeBSD 13.5-RELEASE-p7 1305000 amd64 maintained by: ports@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 517 Nov 22 2024 /usr/ports/biology/exonerate/Makefile Ports top last git commit: 62d8b1999233 Ports top unclean checkout: no Port dir last git commit: 5152f5f9532a Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1305000 Job Id: 09 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1305000 UNAME_v=FreeBSD 13.5-RELEASE-p7 1305000 UNAME_r=13.5-RELEASE-p7 BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/freebsd_13_5_x64-HEAD-ALL/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=tmux-256color OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/freebsd_13_5_x64-HEAD-ALL/09/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_13_5_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_13_5_x64-HEAD-ALL/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- ports@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PKG_CONFIG=pkgconf XDG_DATA_HOME=/wrkdirs/usr/ports/biology/exonerate/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/exonerate/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/exonerate/work/.cache HOME=/wrkdirs/usr/ports/biology/exonerate/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/exonerate/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/exonerate/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288 --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/exonerate/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/exonerate/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/exonerate/work/.cache HOME=/wrkdirs/usr/ports/biology/exonerate/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/exonerate/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/exonerate/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " 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" --End MAKE_ENV-- --PLIST_SUB-- GTK2_VERSION="2.10.0" GTK3_VERSION="3.0.0" GTK4_VERSION="4.0.0" OSREL=13.5 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/exonerate" EXAMPLESDIR="share/examples/exonerate" DATADIR="share/exonerate" WWWDIR="www/exonerate" ETCDIR="etc/exonerate" --End PLIST_SUB-- --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 --End SUB_LIST-- ---Begin make.conf--- DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> NOTICE: The exonerate port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> exonerate-2.4.0_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.4.2_1.pkg [pkg.DaveG.ca] Installing pkg-2.4.2_1... [pkg.DaveG.ca] Extracting pkg-2.4.2_1: .......... done ===> exonerate-2.4.0_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of exonerate-2.4.0_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> NOTICE: The exonerate port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing ===> Fetching all distfiles required by exonerate-2.4.0_1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> NOTICE: The exonerate port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing ===> Fetching all distfiles required by exonerate-2.4.0_1 for building => SHA256 Checksum OK for exonerate-2.4.0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> NOTICE: The exonerate port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing ===> Fetching all distfiles required by exonerate-2.4.0_1 for building ===> Extracting for exonerate-2.4.0_1 => SHA256 Checksum OK for exonerate-2.4.0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for exonerate-2.4.0_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> exonerate-2.4.0_1 depends on package: pkgconf>=1.3.0_1 - not found ===> Installing existing package /packages/All/pkgconf-2.4.3,1.pkg [pkg.DaveG.ca] Installing pkgconf-2.4.3,1... [pkg.DaveG.ca] Extracting pkgconf-2.4.3,1: .......... done ===> exonerate-2.4.0_1 depends on package: pkgconf>=1.3.0_1 - found ===> Returning to build of exonerate-2.4.0_1 ===> exonerate-2.4.0_1 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg.DaveG.ca] Installing ccache-3.7.12_8... [pkg.DaveG.ca] Extracting ccache-3.7.12_8: ......... done Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for clang create symlink for clang (world) create symlink for clang++ create symlink for clang++ (world) ===== Message from ccache-3.7.12_8: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. ===> exonerate-2.4.0_1 depends on file: /usr/local/bin/ccache - found ===> Returning to build of exonerate-2.4.0_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> exonerate-2.4.0_1 depends on shared library: libglib-2.0.so - not found ===> Installing existing package /packages/All/glib-2.84.1_3,2.pkg [pkg.DaveG.ca] Installing glib-2.84.1_3,2... [pkg.DaveG.ca] `-- Installing gettext-runtime-0.23.1... [pkg.DaveG.ca] | `-- Installing indexinfo-0.3.1_1... [pkg.DaveG.ca] | `-- Extracting indexinfo-0.3.1_1: . done [pkg.DaveG.ca] `-- Extracting gettext-runtime-0.23.1: .......... done [pkg.DaveG.ca] `-- Installing libffi-3.5.1... [pkg.DaveG.ca] `-- Extracting libffi-3.5.1: .......... done [pkg.DaveG.ca] `-- Installing libiconv-1.18_1... [pkg.DaveG.ca] `-- Extracting libiconv-1.18_1: .......... done [pkg.DaveG.ca] `-- Installing libinotify-20240724_3... [pkg.DaveG.ca] `-- Extracting libinotify-20240724_3: .......... done [pkg.DaveG.ca] `-- Installing pcre2-10.47_1... [pkg.DaveG.ca] `-- Extracting pcre2-10.47_1: .......... done [pkg.DaveG.ca] `-- Installing py311-packaging-25.0... [pkg.DaveG.ca] | `-- Installing python311-3.11.14... [pkg.DaveG.ca] | | `-- Installing mpdecimal-4.0.1... [pkg.DaveG.ca] | | `-- Extracting mpdecimal-4.0.1: .......... done [pkg.DaveG.ca] | | `-- Installing readline-8.3.1... [pkg.DaveG.ca] | | `-- Extracting readline-8.3.1: .......... done [pkg.DaveG.ca] | `-- Extracting python311-3.11.14: .......... done [pkg.DaveG.ca] `-- Extracting py311-packaging-25.0: .......... done [pkg.DaveG.ca] Extracting glib-2.84.1_3,2: .......... done ==> Running trigger: gio-modules.ucl Generating GIO modules cache ==> Running trigger: glib-schemas.ucl Compiling glib schemas No schema files found: doing nothing. ===== Message from libinotify-20240724_3: -- You might want to consider increasing the kern.maxfiles tunable if you plan to use this library for applications that need to monitor activity of a lot of files. ===== Message from python311-3.11.14: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py311-gdbm databases/py-gdbm@py311 py311-sqlite3 databases/py-sqlite3@py311 py311-tkinter x11-toolkits/py-tkinter@py311 ===> exonerate-2.4.0_1 depends on shared library: libglib-2.0.so - found (/usr/local/lib/libglib-2.0.so) ===> Returning to build of exonerate-2.4.0_1 ===> exonerate-2.4.0_1 depends on shared library: libintl.so - found (/usr/local/lib/libintl.so) =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for exonerate-2.4.0_1 configure: loading site script /usr/ports/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... amd64-portbld-freebsd13.5 checking host system type... amd64-portbld-freebsd13.5 Set host to amd64-portbld-freebsd13.5 amd64-portbld-freebsd13.5 *** Unknown build platform: amd64-portbld-freebsd13.5 *** Set source_root_dir to /wrkdirs/usr/ports/biology/exonerate/work/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 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for exonerate-2.4.0_1 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="\"llu\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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="\"llu\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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="\"llu\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"llu\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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="\"llu\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"llu\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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="\"llu\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"llu\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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="\"llu\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"llu\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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="\"llu\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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:151:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] 151 | g_tree_traverse(rt->recent_data, RangeTree_insert_recent_collect, | ^ /usr/local/include/glib-2.0/glib/gtree.h:147:1: note: 'g_tree_traverse' has been explicitly marked deprecated here 147 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ 1 warning generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"llu\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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="\"llu\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 vfsm.c:38:43: warning: implicit conversion from 'unsigned long' to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Wimplicit-const-int-float-conversion] 38 | if(pow(vfsm->alphabet_size, depth) >= VFSM_MAX){ | ~~ ^~~~~~~~ ./vfsm.h:24:18: note: expanded from macro 'VFSM_MAX' 24 | #define VFSM_MAX G_GINT64_CONSTANT(18446744073709551615U) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/lib/glib-2.0/include/glibconfig.h:69:33: note: expanded from macro 'G_GINT64_CONSTANT' 69 | #define G_GINT64_CONSTANT(val) (val##L) | ^~~~~~ :66:1: note: expanded from here 66 | 18446744073709551615UL | ^~~~~~~~~~~~~~~~~~~~~~ vfsm.c:99:12: warning: format specifies type 'unsigned long long' but the argument has type 'VFSM_Int' (aka 'unsigned long') [-Wformat] 83 | " prs = %" VFSM_PRINT_FORMAT "\n" | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 84 | " prw = %" VFSM_PRINT_FORMAT "\n" | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 85 | " lrs = %" VFSM_PRINT_FORMAT "\n" | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 86 | " lrw = %" VFSM_PRINT_FORMAT "\n" | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 87 | " total = %" VFSM_PRINT_FORMAT "\n", | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 88 | vfsm->alphabet, | ~~~~~~~~~~~~~~~ 89 | vfsm->alphabet_size, | ~~~~~~~~~~~~~~~~~~~~ 90 | vfsm->depth, | ~~~~~~~~~~~~ 91 | vfsm->is_poweroftwo?"TRUE":"FALSE", | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 92 | vfsm->log_alphabet_size, | ~~~~~~~~~~~~~~~~~~~~~~~~ 93 | vfsm->prs, | ^~~~~~~~~~ 94 | vfsm->prw, | ~~~~~~~~~~ 95 | vfsm->lrs, | ~~~~~~~~~~ 96 | vfsm->lrw, | ~~~~~~~~~~ 97 | vfsm->total | ~~~~~~~~~~~ 98 | ); | ~ /usr/local/include/glib-2.0/glib/gmessages.h:358:32: note: expanded from macro 'g_message' 358 | __VA_ARGS__) | ^~~~~~~~~~~ vfsm.c:100:12: warning: format specifies type 'unsigned long long' but the argument has type 'VFSM_Int' (aka 'unsigned long') [-Wformat] 83 | " prs = %" VFSM_PRINT_FORMAT "\n" | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 84 | " prw = %" VFSM_PRINT_FORMAT "\n" | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 85 | " lrs = %" VFSM_PRINT_FORMAT "\n" | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 86 | " lrw = %" VFSM_PRINT_FORMAT "\n" | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 87 | " total = %" VFSM_PRINT_FORMAT "\n", | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 88 | vfsm->alphabet, | ~~~~~~~~~~~~~~~ 89 | vfsm->alphabet_size, | ~~~~~~~~~~~~~~~~~~~~ 90 | vfsm->depth, | ~~~~~~~~~~~~ 91 | vfsm->is_poweroftwo?"TRUE":"FALSE", | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 92 | vfsm->log_alphabet_size, | ~~~~~~~~~~~~~~~~~~~~~~~~ 93 | vfsm->prs, | ~~~~~~~~~~ 94 | vfsm->prw, | ^~~~~~~~~~ 95 | vfsm->lrs, | ~~~~~~~~~~ 96 | vfsm->lrw, | ~~~~~~~~~~ 97 | vfsm->total | ~~~~~~~~~~~ 98 | ); | ~ /usr/local/include/glib-2.0/glib/gmessages.h:358:32: note: expanded from macro 'g_message' 358 | __VA_ARGS__) | ^~~~~~~~~~~ vfsm.c:101:12: warning: format specifies type 'unsigned long long' but the argument has type 'VFSM_Int' (aka 'unsigned long') [-Wformat] 83 | " prs = %" VFSM_PRINT_FORMAT "\n" | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 84 | " prw = %" VFSM_PRINT_FORMAT "\n" | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 85 | " lrs = %" VFSM_PRINT_FORMAT "\n" | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 86 | " lrw = %" VFSM_PRINT_FORMAT "\n" | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 87 | " total = %" VFSM_PRINT_FORMAT "\n", | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 88 | vfsm->alphabet, | ~~~~~~~~~~~~~~~ 89 | vfsm->alphabet_size, | ~~~~~~~~~~~~~~~~~~~~ 90 | vfsm->depth, | ~~~~~~~~~~~~ 91 | vfsm->is_poweroftwo?"TRUE":"FALSE", | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 92 | vfsm->log_alphabet_size, | ~~~~~~~~~~~~~~~~~~~~~~~~ 93 | vfsm->prs, | ~~~~~~~~~~ 94 | vfsm->prw, | ~~~~~~~~~~ 95 | vfsm->lrs, | ^~~~~~~~~~ 96 | vfsm->lrw, | ~~~~~~~~~~ 97 | vfsm->total | ~~~~~~~~~~~ 98 | ); | ~ /usr/local/include/glib-2.0/glib/gmessages.h:358:32: note: expanded from macro 'g_message' 358 | __VA_ARGS__) | ^~~~~~~~~~~ vfsm.c:102:12: warning: format specifies type 'unsigned long long' but the argument has type 'VFSM_Int' (aka 'unsigned long') [-Wformat] 83 | " prs = %" VFSM_PRINT_FORMAT "\n" | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 84 | " prw = %" VFSM_PRINT_FORMAT "\n" | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 85 | " lrs = %" VFSM_PRINT_FORMAT "\n" | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 86 | " lrw = %" VFSM_PRINT_FORMAT "\n" | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 87 | " total = %" VFSM_PRINT_FORMAT "\n", | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 88 | vfsm->alphabet, | ~~~~~~~~~~~~~~~ 89 | vfsm->alphabet_size, | ~~~~~~~~~~~~~~~~~~~~ 90 | vfsm->depth, | ~~~~~~~~~~~~ 91 | vfsm->is_poweroftwo?"TRUE":"FALSE", | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 92 | vfsm->log_alphabet_size, | ~~~~~~~~~~~~~~~~~~~~~~~~ 93 | vfsm->prs, | ~~~~~~~~~~ 94 | vfsm->prw, | ~~~~~~~~~~ 95 | vfsm->lrs, | ~~~~~~~~~~ 96 | vfsm->lrw, | ^~~~~~~~~~ 97 | vfsm->total | ~~~~~~~~~~~ 98 | ); | ~ /usr/local/include/glib-2.0/glib/gmessages.h:358:32: note: expanded from macro 'g_message' 358 | __VA_ARGS__) | ^~~~~~~~~~~ vfsm.c:103:12: warning: format specifies type 'unsigned long long' but the argument has type 'VFSM_Int' (aka 'unsigned long') [-Wformat] 83 | " prs = %" VFSM_PRINT_FORMAT "\n" | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 84 | " prw = %" VFSM_PRINT_FORMAT "\n" | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 85 | " lrs = %" VFSM_PRINT_FORMAT "\n" | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 86 | " lrw = %" VFSM_PRINT_FORMAT "\n" | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 87 | " total = %" VFSM_PRINT_FORMAT "\n", | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 88 | vfsm->alphabet, | ~~~~~~~~~~~~~~~ 89 | vfsm->alphabet_size, | ~~~~~~~~~~~~~~~~~~~~ 90 | vfsm->depth, | ~~~~~~~~~~~~ 91 | vfsm->is_poweroftwo?"TRUE":"FALSE", | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 92 | vfsm->log_alphabet_size, | ~~~~~~~~~~~~~~~~~~~~~~~~ 93 | vfsm->prs, | ~~~~~~~~~~ 94 | vfsm->prw, | ~~~~~~~~~~ 95 | vfsm->lrs, | ~~~~~~~~~~ 96 | vfsm->lrw, | ~~~~~~~~~~ 97 | vfsm->total | ^~~~~~~~~~~ 98 | ); | ~ /usr/local/include/glib-2.0/glib/gmessages.h:358:32: note: expanded from macro 'g_message' 358 | __VA_ARGS__) | ^~~~~~~~~~~ vfsm.c:108:20: warning: format specifies type 'unsigned long long' but the argument has type 'VFSM_Int' (aka 'unsigned long') [-Wformat] 107 | g_print(" branch_size [%d] [%" VFSM_PRINT_FORMAT "]\n", | ~~~~~~~~~~~~~~~~~~~~ 108 | i, vfsm->branch_size[i]); | ^~~~~~~~~~~~~~~~~~~~ 7 warnings generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"llu\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"llu\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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="\"llu\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"llu\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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="\"llu\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"llu\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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="\"llu\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"llu\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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="\"llu\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"llu\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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="\"llu\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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:138:13: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 138 | if(!g_strcasecmp(arg_string, true_string[i])) | ^ /usr/local/include/glib-2.0/glib/gstrfuncs.h:267:1: note: 'g_strcasecmp' has been explicitly marked deprecated here 267 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ argument.c:140:13: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 140 | if(!g_strcasecmp(arg_string, false_string[i])) | ^ /usr/local/include/glib-2.0/glib/gstrfuncs.h:267:1: note: 'g_strcasecmp' has been explicitly marked deprecated here 267 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ argument.c:306:9: warning: Deprecated pre-processor symbol [-W#pragma-messages] 306 | if(!g_thread_supported()) | ^ /usr/local/include/glib-2.0/glib/deprecated/gthread.h:280:38: note: expanded from macro 'g_thread_supported' 280 | #define g_thread_supported() (1) GLIB_DEPRECATED_MACRO_IN_2_32 | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:141:39: note: expanded from macro 'GLIB_DEPRECATED_MACRO_IN_2_32' 141 | #define GLIB_DEPRECATED_MACRO_IN_2_32 GLIB_DEPRECATED_MACRO | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1302:31: note: expanded from macro 'GLIB_DEPRECATED_MACRO' 1302 | #define GLIB_DEPRECATED_MACRO _GLIB_GNUC_DO_PRAGMA(GCC warning "Deprecated pre-processor symbol") | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1301:33: note: expanded from macro '_GLIB_GNUC_DO_PRAGMA' 1301 | #define _GLIB_GNUC_DO_PRAGMA(x) _Pragma(G_STRINGIFY (x)) | ^ :154:6: note: expanded from here 154 | GCC warning "Deprecated pre-processor symbol" | ^ argument.c:307:9: warning: 'g_thread_init' is deprecated [-Wdeprecated-declarations] 307 | g_thread_init(NULL); | ^ /usr/local/include/glib-2.0/glib/deprecated/gthread.h:270:1: note: 'g_thread_init' has been explicitly marked deprecated here 270 | GLIB_DEPRECATED_IN_2_32 | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:139:33: note: expanded from macro 'GLIB_DEPRECATED_IN_2_32' 139 | #define GLIB_DEPRECATED_IN_2_32 GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ argument.c:502:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] 502 | g_tree_traverse(arg->option_registry, Argument_set_env_var_func, | ^ /usr/local/include/glib-2.0/glib/gtree.h:147:1: note: 'g_tree_traverse' has been explicitly marked deprecated here 147 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ argument.c:559:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] 559 | g_tree_traverse(arg->option_registry, | ^ /usr/local/include/glib-2.0/glib/gtree.h:147:1: note: 'g_tree_traverse' has been explicitly marked deprecated here 147 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ 6 warnings generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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:168:9: warning: Deprecated pre-processor symbol: replace with "g_string_append_printf" [-W#pragma-messages] 168 | g_string_sprintfa(full_msg, "linecount: %d\n", line_count+1); | ^ /usr/local/include/glib-2.0/glib/gstring.h:296:51: note: expanded from macro 'g_string_sprintfa' 296 | #define g_string_sprintfa g_string_append_printf GLIB_DEPRECATED_MACRO_IN_2_26_FOR(g_string_append_printf) | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:40:46: note: expanded from macro 'GLIB_DEPRECATED_MACRO_IN_2_26_FOR' 40 | #define GLIB_DEPRECATED_MACRO_IN_2_26_FOR(f) GLIB_DEPRECATED_MACRO_FOR (f) | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1304:3: note: expanded from macro 'GLIB_DEPRECATED_MACRO_FOR' 1304 | _GLIB_GNUC_DO_PRAGMA(GCC warning G_STRINGIFY (Deprecated pre-processor symbol: replace with #f)) | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1301:33: note: expanded from macro '_GLIB_GNUC_DO_PRAGMA' 1301 | #define _GLIB_GNUC_DO_PRAGMA(x) _Pragma(G_STRINGIFY (x)) | ^ :83:6: note: expanded from here 83 | GCC warning "Deprecated pre-processor symbol: replace with \"g_string_append_printf\"" | ^ socket.c:169:5: warning: Deprecated pre-processor symbol: replace with "g_string_append_printf" [-W#pragma-messages] 169 | g_string_sprintfa(full_msg, "%s", msg); | ^ /usr/local/include/glib-2.0/glib/gstring.h:296:51: note: expanded from macro 'g_string_sprintfa' 296 | #define g_string_sprintfa g_string_append_printf GLIB_DEPRECATED_MACRO_IN_2_26_FOR(g_string_append_printf) | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:40:46: note: expanded from macro 'GLIB_DEPRECATED_MACRO_IN_2_26_FOR' 40 | #define GLIB_DEPRECATED_MACRO_IN_2_26_FOR(f) GLIB_DEPRECATED_MACRO_FOR (f) | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1304:3: note: expanded from macro 'GLIB_DEPRECATED_MACRO_FOR' 1304 | _GLIB_GNUC_DO_PRAGMA(GCC warning G_STRINGIFY (Deprecated pre-processor symbol: replace with #f)) | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1301:33: note: expanded from macro '_GLIB_GNUC_DO_PRAGMA' 1301 | #define _GLIB_GNUC_DO_PRAGMA(x) _Pragma(G_STRINGIFY (x)) | ^ :88:6: note: expanded from here 88 | GCC warning "Deprecated pre-processor symbol: replace with \"g_string_append_printf\"" | ^ 2 warnings generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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:34:9: warning: Deprecated pre-processor symbol [-W#pragma-messages] 34 | if(!g_thread_supported()) | ^ /usr/local/include/glib-2.0/glib/deprecated/gthread.h:280:38: note: expanded from macro 'g_thread_supported' 280 | #define g_thread_supported() (1) GLIB_DEPRECATED_MACRO_IN_2_32 | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:141:39: note: expanded from macro 'GLIB_DEPRECATED_MACRO_IN_2_32' 141 | #define GLIB_DEPRECATED_MACRO_IN_2_32 GLIB_DEPRECATED_MACRO | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1302:31: note: expanded from macro 'GLIB_DEPRECATED_MACRO' 1302 | #define GLIB_DEPRECATED_MACRO _GLIB_GNUC_DO_PRAGMA(GCC warning "Deprecated pre-processor symbol") | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1301:33: note: expanded from macro '_GLIB_GNUC_DO_PRAGMA' 1301 | #define _GLIB_GNUC_DO_PRAGMA(x) _Pragma(G_STRINGIFY (x)) | ^ :63:6: note: expanded from here 63 | GCC warning "Deprecated pre-processor symbol" | ^ jobqueue.test.c:35:9: warning: 'g_thread_init' is deprecated [-Wdeprecated-declarations] 35 | g_thread_init(NULL); | ^ /usr/local/include/glib-2.0/glib/deprecated/gthread.h:270:1: note: 'g_thread_init' has been explicitly marked deprecated here 270 | GLIB_DEPRECATED_IN_2_32 | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:139:33: note: expanded from macro 'GLIB_DEPRECATED_IN_2_32' 139 | #define GLIB_DEPRECATED_IN_2_32 GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ 2 warnings generated. cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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:97:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] 97 | g_tree_traverse(tree, Sequence_destroy_annotation_data, | ^ /usr/local/include/glib-2.0/glib/gtree.h:147:1: note: 'g_tree_traverse' has been explicitly marked deprecated here 147 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ 1 warning generated. cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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:317:13: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 317 | if(!g_strcasecmp(name, dna_string[i])) | ^ /usr/local/include/glib-2.0/glib/gstrfuncs.h:267:1: note: 'g_strcasecmp' has been explicitly marked deprecated here 267 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ alphabet.c:320:13: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 320 | if(!g_strcasecmp(name, protein_string[i])) | ^ /usr/local/include/glib-2.0/glib/gstrfuncs.h:267:1: note: 'g_strcasecmp' has been explicitly marked deprecated here 267 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ alphabet.c:323:13: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 323 | if(!g_strcasecmp(name, unknown_string[i])) | ^ /usr/local/include/glib-2.0/glib/gstrfuncs.h:267:1: note: 'g_strcasecmp' has been explicitly marked deprecated here 267 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ 3 warnings generated. cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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:146:21: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 146 | if(!g_strcasecmp(word, "splice")) | ^ /usr/local/include/glib-2.0/glib/gstrfuncs.h:267:1: note: 'g_strcasecmp' has been explicitly marked deprecated here 267 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ splice.c:195:40: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 195 | if((!path) || (!strlen(path)) || (!g_strcasecmp(path, "primate"))) | ^ /usr/local/include/glib-2.0/glib/gstrfuncs.h:267:1: note: 'g_strcasecmp' has been explicitly marked deprecated here 267 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ splice.c:203:40: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 203 | if((!path) || (!strlen(path)) || (!g_strcasecmp(path, "primate"))) | ^ /usr/local/include/glib-2.0/glib/gstrfuncs.h:267:1: note: 'g_strcasecmp' has been explicitly marked deprecated here 267 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ 3 warnings generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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:637:9: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] 637 | g_strdown(query_str); | ^ /usr/local/include/glib-2.0/glib/gstrfuncs.h:274:1: note: 'g_strdown' has been explicitly marked deprecated here 274 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ hspset.c:638:9: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] 638 | g_strdown(target_str); | ^ /usr/local/include/glib-2.0/glib/gstrfuncs.h:274:1: note: 'g_strdown' has been explicitly marked deprecated here 274 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ hspset.c:640:9: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] 640 | g_strup(query_str); | ^ /usr/local/include/glib-2.0/glib/gstrfuncs.h:276:1: note: 'g_strup' has been explicitly marked deprecated here 276 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ hspset.c:641:9: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] 641 | g_strup(target_str); | ^ /usr/local/include/glib-2.0/glib/gstrfuncs.h:276:1: note: 'g_strup' has been explicitly marked deprecated here 276 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ 4 warnings generated. cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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:31:21: warning: 'g_mem_chunk_alloc' is deprecated [-Wdeprecated-declarations] 31 | pcr_match = g_chunk_new(PCR_Match, pcr->match_mem_chunk); | ^ /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:36:51: note: expanded from macro 'g_chunk_new' 36 | #define g_chunk_new(type, chunk) ((type *) g_mem_chunk_alloc (chunk)) | ^ /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:49:1: note: 'g_mem_chunk_alloc' has been explicitly marked deprecated here 49 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ pcr.c:59:37: warning: 'g_mem_chunk_alloc' is deprecated [-Wdeprecated-declarations] 59 | register PCR_Probe *pcr_probe = g_chunk_new(PCR_Probe, | ^ /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:36:51: note: expanded from macro 'g_chunk_new' 36 | #define g_chunk_new(type, chunk) ((type *) g_mem_chunk_alloc (chunk)) | ^ /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:49:1: note: 'g_mem_chunk_alloc' has been explicitly marked deprecated here 49 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ pcr.c:69:5: warning: 'g_mem_chunk_free' is deprecated [-Wdeprecated-declarations] 69 | g_mem_chunk_free(pcr->probe_mem_chunk, pcr_probe); | ^ /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:53:1: note: 'g_mem_chunk_free' has been explicitly marked deprecated here 53 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ pcr.c:155:39: warning: 'g_mem_chunk_alloc' is deprecated [-Wdeprecated-declarations] 155 | register PCR_Sensor *pcr_sensor = g_chunk_new(PCR_Sensor, | ^ /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:36:51: note: expanded from macro 'g_chunk_new' 36 | #define g_chunk_new(type, chunk) ((type *) g_mem_chunk_alloc (chunk)) | ^ /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:49:1: note: 'g_mem_chunk_alloc' has been explicitly marked deprecated here 49 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ pcr.c:174:5: warning: 'g_mem_chunk_free' is deprecated [-Wdeprecated-declarations] 174 | g_mem_chunk_free(pcr->sensor_mem_chunk, pcr_sensor); | ^ /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:53:1: note: 'g_mem_chunk_free' has been explicitly marked deprecated here 53 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ pcr.c:252:5: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] 252 | g_strup(pcr_primer->forward); | ^ /usr/local/include/glib-2.0/glib/gstrfuncs.h:276:1: note: 'g_strup' has been explicitly marked deprecated here 276 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ pcr.c:253:5: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] 253 | g_strup(pcr_primer->revcomp); | ^ /usr/local/include/glib-2.0/glib/gstrfuncs.h:276:1: note: 'g_strup' has been explicitly marked deprecated here 276 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ pcr.c:357:29: warning: 'g_mem_chunk_new' is deprecated [-Wdeprecated-declarations] 357 | pcr->sensor_mem_chunk = g_mem_chunk_new("PCR_Sensor", | ^ /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:42:1: note: 'g_mem_chunk_new' has been explicitly marked deprecated here 42 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ pcr.c:363:28: warning: 'g_mem_chunk_new' is deprecated [-Wdeprecated-declarations] 363 | pcr->probe_mem_chunk = g_mem_chunk_new("PCR_Probe", | ^ /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:42:1: note: 'g_mem_chunk_new' has been explicitly marked deprecated here 42 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ pcr.c:366:28: warning: 'g_mem_chunk_new' is deprecated [-Wdeprecated-declarations] 366 | pcr->match_mem_chunk = g_mem_chunk_new("PCR_Match", | ^ /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:42:1: note: 'g_mem_chunk_new' has been explicitly marked deprecated here 42 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ pcr.c:381:5: warning: 'g_mem_chunk_destroy' is deprecated [-Wdeprecated-declarations] 381 | g_mem_chunk_destroy(pcr->sensor_mem_chunk); | ^ /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:47:1: note: 'g_mem_chunk_destroy' has been explicitly marked deprecated here 47 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ pcr.c:383:5: warning: 'g_mem_chunk_destroy' is deprecated [-Wdeprecated-declarations] 383 | g_mem_chunk_destroy(pcr->probe_mem_chunk); | ^ /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:47:1: note: 'g_mem_chunk_destroy' has been explicitly marked deprecated here 47 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ pcr.c:384:5: warning: 'g_mem_chunk_destroy' is deprecated [-Wdeprecated-declarations] 384 | g_mem_chunk_destroy(pcr->match_mem_chunk); | ^ /usr/local/include/glib-2.0/glib/deprecated/gallocator.h:47:1: note: 'g_mem_chunk_destroy' has been explicitly marked deprecated here 47 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ 13 warnings generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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:268:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 268 | if(!g_strcasecmp(force_fsm, "none")) | ^ /usr/local/include/glib-2.0/glib/gstrfuncs.h:267:1: note: 'g_strcasecmp' has been explicitly marked deprecated here 267 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ seeder.c:273:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 273 | if(!g_strcasecmp(force_fsm, "normal")) | ^ /usr/local/include/glib-2.0/glib/gstrfuncs.h:267:1: note: 'g_strcasecmp' has been explicitly marked deprecated here 267 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ seeder.c:275:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 275 | if(!g_strcasecmp(force_fsm, "compact")) | ^ /usr/local/include/glib-2.0/glib/gstrfuncs.h:267:1: note: 'g_strcasecmp' has been explicitly marked deprecated here 267 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ 3 warnings generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"llu\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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="\"llu\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"llu\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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="\"llu\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"llu\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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="\"llu\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 dataset.c:316:13: warning: format specifies type 'long long' but the argument has type 'guint64' (aka 'unsigned long') [-Wformat] 310 | " number of sequences: %lld\n" | ~~~~ | %lu 311 | " longest sequence: %lld\n\n", 312 | (gint)dataset->header->version, 313 | (dataset->header->type & 1)?"DNA":"PROTEIN", 314 | (dataset->header->type & 2)?"masked":"unmasked", 315 | (gint)(dataset->header->total_db_len >> 20), 316 | dataset->header->number_of_seqs, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dataset.c:317:13: warning: format specifies type 'long long' but the argument has type 'guint64' (aka 'unsigned long') [-Wformat] 311 | " longest sequence: %lld\n\n", | ~~~~ | %lu 312 | (gint)dataset->header->version, 313 | (dataset->header->type & 1)?"DNA":"PROTEIN", 314 | (dataset->header->type & 2)?"masked":"unmasked", 315 | (gint)(dataset->header->total_db_len >> 20), 316 | dataset->header->number_of_seqs, 317 | dataset->header->max_seq_len); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2 warnings generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"llu\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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="\"llu\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 index.c:379:15: warning: format specifies type 'unsigned long long' but the argument has type 'gint64' (aka 'long') [-Wformat] 377 | g_message("Removed [%" CUSTOM_GUINT64_FORMAT | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 378 | "] words, [%" CUSTOM_GUINT64_FORMAT "] instances", | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 379 | removed_words, removed_instances); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/include/glib-2.0/glib/gmessages.h:358:32: note: expanded from macro 'g_message' 358 | __VA_ARGS__) | ^~~~~~~~~~~ index.c:379:30: warning: format specifies type 'unsigned long long' but the argument has type 'gint64' (aka 'long') [-Wformat] 377 | g_message("Removed [%" CUSTOM_GUINT64_FORMAT | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 378 | "] words, [%" CUSTOM_GUINT64_FORMAT "] instances", | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 379 | removed_words, removed_instances); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /usr/local/include/glib-2.0/glib/gmessages.h:358:32: note: expanded from macro 'g_message' 358 | __VA_ARGS__) | ^~~~~~~~~~~ 2 warnings generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-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="\"amd64-portbld-freebsd13.5\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-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="\"amd64-portbld-freebsd13.5\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-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="\"amd64-portbld-freebsd13.5\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-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="\"amd64-portbld-freebsd13.5\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-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="\"amd64-portbld-freebsd13.5\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-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="\"amd64-portbld-freebsd13.5\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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:660:9: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] 660 | g_strdown(qy_seq_string); | ^ /usr/local/include/glib-2.0/glib/gstrfuncs.h:274:1: note: 'g_strdown' has been explicitly marked deprecated here 274 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ alignment.c:667:9: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] 667 | g_strdown(tg_seq_string); | ^ /usr/local/include/glib-2.0/glib/gstrfuncs.h:274:1: note: 'g_strdown' has been explicitly marked deprecated here 274 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ alignment.c:677:13: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] 677 | g_strdown(qy_seq_string); | ^ /usr/local/include/glib-2.0/glib/gstrfuncs.h:274:1: note: 'g_strdown' has been explicitly marked deprecated here 274 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ alignment.c:690:9: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] 690 | g_strdown(tg_seq_string); | ^ /usr/local/include/glib-2.0/glib/gstrfuncs.h:274:1: note: 'g_strdown' has been explicitly marked deprecated here 274 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ alignment.c:987:5: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] 987 | g_strup(qy_codon); | ^ /usr/local/include/glib-2.0/glib/gstrfuncs.h:276:1: note: 'g_strup' has been explicitly marked deprecated here 276 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ alignment.c:988:5: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] 988 | g_strup(tg_codon); | ^ /usr/local/include/glib-2.0/glib/gstrfuncs.h:276:1: note: 'g_strup' has been explicitly marked deprecated here 276 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ 6 warnings generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-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="\"amd64-portbld-freebsd13.5\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-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="\"amd64-portbld-freebsd13.5\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-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="\"amd64-portbld-freebsd13.5\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-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="\"amd64-portbld-freebsd13.5\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-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="\"amd64-portbld-freebsd13.5\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-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="\"amd64-portbld-freebsd13.5\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 viterbi.c:877:22: warning: equality comparison with extraneous parentheses [-Wparentheses-equality] 877 | if((macro[i] == '%')){ | ~~~~~~~~~^~~~~~ viterbi.c:877:22: note: remove extraneous parentheses around the comparison to silence this warning 877 | if((macro[i] == '%')){ | ~ ^ ~ viterbi.c:877:22: note: use '=' to turn this equality comparison into an assignment 877 | if((macro[i] == '%')){ | ^~ | = 1 warning generated. cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-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="\"amd64-portbld-freebsd13.5\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-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="\"amd64-portbld-freebsd13.5\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-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="\"amd64-portbld-freebsd13.5\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-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="\"amd64-portbld-freebsd13.5\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-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="\"amd64-portbld-freebsd13.5\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-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="\"amd64-portbld-freebsd13.5\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-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="\"amd64-portbld-freebsd13.5\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-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="\"amd64-portbld-freebsd13.5\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-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="\"amd64-portbld-freebsd13.5\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-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="\"amd64-portbld-freebsd13.5\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 heuristic.c:759:44: warning: if statement has empty body [-Wempty-body] 759 | if((*max_query_join_range) < range); | ^ heuristic.c:759:44: note: put the semicolon on a separate line to silence this warning heuristic.c:762:45: warning: if statement has empty body [-Wempty-body] 762 | if((*max_target_join_range) < range); | ^ heuristic.c:762:45: note: put the semicolon on a separate line to silence this warning 2 warnings generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-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="\"amd64-portbld-freebsd13.5\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-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="\"amd64-portbld-freebsd13.5\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-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="\"amd64-portbld-freebsd13.5\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-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="\"amd64-portbld-freebsd13.5\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-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="\"amd64-portbld-freebsd13.5\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-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="\"amd64-portbld-freebsd13.5\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-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="\"amd64-portbld-freebsd13.5\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-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="\"amd64-portbld-freebsd13.5\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-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="\"amd64-portbld-freebsd13.5\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-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="\"amd64-portbld-freebsd13.5\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-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="\"amd64-portbld-freebsd13.5\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-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="\"amd64-portbld-freebsd13.5\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-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="\"amd64-portbld-freebsd13.5\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-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="\"amd64-portbld-freebsd13.5\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-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="\"amd64-portbld-freebsd13.5\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-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="\"amd64-portbld-freebsd13.5\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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:121:13: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 121 | if(!g_strcasecmp(name[i], str)) | ^ /usr/local/include/glib-2.0/glib/gstrfuncs.h:267:1: note: 'g_strcasecmp' has been explicitly marked deprecated here 267 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ modeltype.c:124:13: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 124 | if(!g_strcasecmp(short_name[i], str)) | ^ /usr/local/include/glib-2.0/glib/gstrfuncs.h:267:1: note: 'g_strcasecmp' has been explicitly marked deprecated here 267 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ 2 warnings generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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:421:23: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 421 | if((!models) || (!g_strcasecmp(models, "all"))) | ^ /usr/local/include/glib-2.0/glib/gstrfuncs.h:267:1: note: 'g_strcasecmp' has been explicitly marked deprecated here 267 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ 1 warning generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"amd64-portbld-freebsd13.5\"" -DSOURCE_ROOT_DIR="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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="\"amd64-portbld-freebsd13.5\"" -DSOURCE_ROOT_DIR="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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:68:13: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 68 | if(!g_strcasecmp(name[i], str)) | ^ /usr/local/include/glib-2.0/glib/gstrfuncs.h:267:1: note: 'g_strcasecmp' has been explicitly marked deprecated here 267 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ gam.c:526:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] 526 | g_tree_traverse(bestn_tree, GAM_tree_collect_values, | ^ /usr/local/include/glib-2.0/glib/gtree.h:147:1: note: 'g_tree_traverse' has been explicitly marked deprecated here 147 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ gam.c:539:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] 539 | g_tree_traverse(percent_threshold_tree, GAM_tree_collect_values, | ^ /usr/local/include/glib-2.0/glib/gtree.h:147:1: note: 'g_tree_traverse' has been explicitly marked deprecated here 147 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ gam.c:589:9: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] 589 | g_tree_traverse(gam->bestn_tree, GAM_bestn_tree_report_traverse, | ^ /usr/local/include/glib-2.0/glib/gtree.h:147:1: note: 'g_tree_traverse' has been explicitly marked deprecated here 147 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ 4 warnings generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"amd64-portbld-freebsd13.5\"" -DSOURCE_ROOT_DIR="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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="\"amd64-portbld-freebsd13.5\"" -DSOURCE_ROOT_DIR="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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:329:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 329 | if(!g_strcasecmp(force_scan, "none")){ | ^ /usr/local/include/glib-2.0/glib/gstrfuncs.h:267:1: note: 'g_strcasecmp' has been explicitly marked deprecated here 267 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ analysis.c:336:17: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 336 | } else if((!g_strcasecmp(force_scan, "query")) | ^ /usr/local/include/glib-2.0/glib/gstrfuncs.h:267:1: note: 'g_strcasecmp' has been explicitly marked deprecated here 267 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ analysis.c:337:17: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 337 | || (!g_strcasecmp(force_scan, "q"))){ | ^ /usr/local/include/glib-2.0/glib/gstrfuncs.h:267:1: note: 'g_strcasecmp' has been explicitly marked deprecated here 267 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ analysis.c:339:17: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 339 | } else if((!g_strcasecmp(force_scan, "target")) | ^ /usr/local/include/glib-2.0/glib/gstrfuncs.h:267:1: note: 'g_strcasecmp' has been explicitly marked deprecated here 267 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ analysis.c:340:17: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 340 | || (!g_strcasecmp(force_scan, "t"))){ | ^ /usr/local/include/glib-2.0/glib/gstrfuncs.h:267:1: note: 'g_strcasecmp' has been explicitly marked deprecated here 267 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ 5 warnings generated. cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_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="\"amd64-portbld-freebsd13.5\"" -DSOURCE_ROOT_DIR="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"amd64-portbld-freebsd13.5\"" -DSOURCE_ROOT_DIR="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"amd64-portbld-freebsd13.5\"" -DSOURCE_ROOT_DIR="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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: 19:31:43.848: Starting building bootstrapping components ** Message: 19:31:43.849: Processing model [u] ** Message: 19:31:43.849: Bootstrapper processing model [ungapped:dna2dna] ** Message: 19:31:43.850: Process optimal [optimal:ungapped:dna2dna] ** (process:30471): WARNING **: 19:31:43.850: Creating codegen directory [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen] ** (process:30471): WARNING **: 19:31:43.850: Creating codegen directory [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen] ** (process:30471): WARNING **: 19:31:43.850: Creating codegen directory [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5] ** (process:30471): WARNING **: 19:31:43.850: Creating codegen directory [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5] ** Message: 19:31:43.850: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_dna2dna_32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_dna2dna_32_find_32_score.c ** Message: 19:31:44.050: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_dna2dna_32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_dna2dna_32_find_32_path.c ** Message: 19:31:44.257: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_dna2dna_32_find_32_region.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_dna2dna_32_find_32_region.c ** Message: 19:31:44.492: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.c ** Message: 19:31:44.727: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 19:31:44.963: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_dna2dna_32_find_32_score.o] ** Message: 19:31:44.963: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_dna2dna_32_find_32_score.o] to archive ar -cSq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_dna2dna_32_find_32_score.o ** Message: 19:31:44.966: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_score] ** Message: 19:31:44.966: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_dna2dna_32_find_32_path.o] ** Message: 19:31:44.966: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_dna2dna_32_find_32_path.o ** Message: 19:31:44.968: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_path] ** Message: 19:31:44.968: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_dna2dna_32_find_32_region.o] ** Message: 19:31:44.968: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_dna2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_dna2dna_32_find_32_region.o ** Message: 19:31:44.972: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_region] ** Message: 19:31:44.972: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.o] ** Message: 19:31:44.972: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.o ** Message: 19:31:44.976: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint] ** Message: 19:31:44.976: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 19:31:44.976: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 19:31:44.980: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation] ** Message: 19:31:44.980: Bootstrapper processing model [ungapped:protein2protein] ** Message: 19:31:44.980: Process optimal [optimal:ungapped:protein2protein] ** Message: 19:31:44.980: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_protein2protein_32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_protein2protein_32_find_32_score.c ** Message: 19:31:45.182: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_protein2protein_32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_protein2protein_32_find_32_path.c ** Message: 19:31:45.387: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_protein2protein_32_find_32_region.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_protein2protein_32_find_32_region.c ** Message: 19:31:45.619: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.c ** Message: 19:31:45.863: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.c ** Message: 19:31:46.129: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_protein2protein_32_find_32_score.o] ** Message: 19:31:46.129: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_protein2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_protein2protein_32_find_32_score.o ** Message: 19:31:46.133: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_score] ** Message: 19:31:46.133: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_protein2protein_32_find_32_path.o] ** Message: 19:31:46.133: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_protein2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_protein2protein_32_find_32_path.o ** Message: 19:31:46.135: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_path] ** Message: 19:31:46.135: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_protein2protein_32_find_32_region.o] ** Message: 19:31:46.135: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_protein2protein_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_protein2protein_32_find_32_region.o ** Message: 19:31:46.138: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_region] ** Message: 19:31:46.138: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.o] ** Message: 19:31:46.138: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.o ** Message: 19:31:46.141: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint] ** Message: 19:31:46.141: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.o] ** Message: 19:31:46.141: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.o ** Message: 19:31:46.147: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation] ** Message: 19:31:46.147: Bootstrapper processing model [ungapped:dna2protein] ** Message: 19:31:46.147: Process optimal [optimal:ungapped:dna2protein] ** Message: 19:31:46.147: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_dna2protein_32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_dna2protein_32_find_32_score.c ** Message: 19:31:46.400: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_dna2protein_32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_dna2protein_32_find_32_path.c ** Message: 19:31:46.645: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_dna2protein_32_find_32_region.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_dna2protein_32_find_32_region.c ** Message: 19:31:46.875: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.c ** Message: 19:31:47.154: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.c ** Message: 19:31:47.445: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_dna2protein_32_find_32_score.o] ** Message: 19:31:47.445: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_dna2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_dna2protein_32_find_32_score.o ** Message: 19:31:47.449: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_score] ** Message: 19:31:47.449: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_dna2protein_32_find_32_path.o] ** Message: 19:31:47.449: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_dna2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_dna2protein_32_find_32_path.o ** Message: 19:31:47.452: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_path] ** Message: 19:31:47.452: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_dna2protein_32_find_32_region.o] ** Message: 19:31:47.452: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_dna2protein_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_dna2protein_32_find_32_region.o ** Message: 19:31:47.455: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_region] ** Message: 19:31:47.455: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.o] ** Message: 19:31:47.455: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.o ** Message: 19:31:47.458: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint] ** Message: 19:31:47.458: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.o] ** Message: 19:31:47.458: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.o ** Message: 19:31:47.461: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation] ** Message: 19:31:47.461: Bootstrapper processing model [ungapped:protein2dna] ** Message: 19:31:47.462: Process optimal [optimal:ungapped:protein2dna] ** Message: 19:31:47.462: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_protein2dna_32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_protein2dna_32_find_32_score.c ** Message: 19:31:47.700: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_protein2dna_32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_protein2dna_32_find_32_path.c ** Message: 19:31:47.921: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_protein2dna_32_find_32_region.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_protein2dna_32_find_32_region.c ** Message: 19:31:48.176: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.c ** Message: 19:31:48.513: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.c ** Message: 19:31:48.851: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_protein2dna_32_find_32_score.o] ** Message: 19:31:48.852: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_protein2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_protein2dna_32_find_32_score.o ** Message: 19:31:48.856: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_score] ** Message: 19:31:48.856: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_protein2dna_32_find_32_path.o] ** Message: 19:31:48.856: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_protein2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_protein2dna_32_find_32_path.o ** Message: 19:31:48.860: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_path] ** Message: 19:31:48.860: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_protein2dna_32_find_32_region.o] ** Message: 19:31:48.860: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_protein2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_protein2dna_32_find_32_region.o ** Message: 19:31:48.863: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_region] ** Message: 19:31:48.863: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.o] ** Message: 19:31:48.863: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.o ** Message: 19:31:48.867: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint] ** Message: 19:31:48.867: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.o] ** Message: 19:31:48.867: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.o ** Message: 19:31:48.870: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation] ** Message: 19:31:48.870: Processing model [u:t] ** Message: 19:31:48.871: Bootstrapper processing model [ungapped:codon] ** Message: 19:31:48.871: Process optimal [optimal:ungapped:codon] ** Message: 19:31:48.871: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_codon_32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_codon_32_find_32_score.c ** Message: 19:31:49.247: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_codon_32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_codon_32_find_32_path.c ** Message: 19:31:49.640: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_codon_32_find_32_region.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_codon_32_find_32_region.c ** Message: 19:31:50.051: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_codon_32_find_32_checkpoint.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_codon_32_find_32_checkpoint.c ** Message: 19:31:50.591: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.c ** Message: 19:31:51.093: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_codon_32_find_32_score.o] ** Message: 19:31:51.095: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_codon_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_codon_32_find_32_score.o ** Message: 19:31:51.120: Adding function [optimal_58_ungapped_58_codon_32_find_32_score] ** Message: 19:31:51.120: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_codon_32_find_32_path.o] ** Message: 19:31:51.120: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_codon_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_codon_32_find_32_path.o ** Message: 19:31:51.131: Adding function [optimal_58_ungapped_58_codon_32_find_32_path] ** Message: 19:31:51.131: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_codon_32_find_32_region.o] ** Message: 19:31:51.131: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_codon_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_codon_32_find_32_region.o ** Message: 19:31:51.138: Adding function [optimal_58_ungapped_58_codon_32_find_32_region] ** Message: 19:31:51.138: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_codon_32_find_32_checkpoint.o] ** Message: 19:31:51.138: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_codon_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_codon_32_find_32_checkpoint.o ** Message: 19:31:51.155: Adding function [optimal_58_ungapped_58_codon_32_find_32_checkpoint] ** Message: 19:31:51.155: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.o] ** Message: 19:31:51.155: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.o ** Message: 19:31:51.159: Adding function [optimal_58_ungapped_58_codon_32_find_32_path_32_continuation] ** Message: 19:31:51.160: Processing model [a:g] ** Message: 19:31:51.160: Bootstrapper processing model [affine:global:dna2dna] ** Message: 19:31:51.160: Process optimal [optimal:affine:global:dna2dna] ** Message: 19:31:51.161: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.c ** Message: 19:31:51.621: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.c ** Message: 19:31:52.009: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.c ** Message: 19:31:52.400: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 19:31:52.804: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.o] ** Message: 19:31:52.804: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.o ** Message: 19:31:52.809: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_score] ** Message: 19:31:52.809: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.o] ** Message: 19:31:52.809: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.o ** Message: 19:31:52.813: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_path] ** Message: 19:31:52.813: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.o] ** Message: 19:31:52.813: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.o ** Message: 19:31:52.816: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint] ** Message: 19:31:52.816: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 19:31:52.816: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 19:31:52.819: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation] ** Message: 19:31:52.820: Bootstrapper processing model [affine:global:protein2protein] ** Message: 19:31:52.820: Process optimal [optimal:affine:global:protein2protein] ** Message: 19:31:52.820: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.c ** Message: 19:31:53.114: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.c ** Message: 19:31:53.650: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.c ** Message: 19:31:54.001: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.c ** Message: 19:31:54.340: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.o] ** Message: 19:31:54.340: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.o ** Message: 19:31:54.343: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_score] ** Message: 19:31:54.343: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.o] ** Message: 19:31:54.343: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.o ** Message: 19:31:54.346: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_path] ** Message: 19:31:54.346: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.o] ** Message: 19:31:54.346: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.o ** Message: 19:31:54.352: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint] ** Message: 19:31:54.352: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.o] ** Message: 19:31:54.352: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.o ** Message: 19:31:54.357: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation] ** Message: 19:31:54.357: Processing model [a:b] ** Message: 19:31:54.357: Bootstrapper processing model [affine:bestfit:dna2dna] ** Message: 19:31:54.357: Process optimal [optimal:affine:bestfit:dna2dna] ** Message: 19:31:54.358: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.c ** Message: 19:31:54.738: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.c ** Message: 19:31:55.227: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.c ** Message: 19:31:55.863: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.c ** Message: 19:31:56.302: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 19:31:56.876: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.o] ** Message: 19:31:56.876: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.o ** Message: 19:31:56.881: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score] ** Message: 19:31:56.881: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.o] ** Message: 19:31:56.881: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.o ** Message: 19:31:56.887: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path] ** Message: 19:31:56.887: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.o] ** Message: 19:31:56.887: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.o ** Message: 19:31:56.893: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region] ** Message: 19:31:56.893: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.o] ** Message: 19:31:56.893: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.o ** Message: 19:31:56.900: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint] ** Message: 19:31:56.900: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 19:31:56.900: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 19:31:56.907: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation] ** Message: 19:31:56.908: Bootstrapper processing model [affine:bestfit:protein2protein] ** Message: 19:31:56.908: Process optimal [optimal:affine:bestfit:protein2protein] ** Message: 19:31:56.909: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.c ** Message: 19:31:57.388: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.c ** Message: 19:31:57.864: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.c ** Message: 19:31:58.319: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.c ** Message: 19:31:58.699: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.c ** Message: 19:31:59.241: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.o] ** Message: 19:31:59.241: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.o ** Message: 19:31:59.249: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score] ** Message: 19:31:59.249: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.o] ** Message: 19:31:59.250: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.o ** Message: 19:31:59.256: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path] ** Message: 19:31:59.256: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.o] ** Message: 19:31:59.256: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.o ** Message: 19:31:59.263: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region] ** Message: 19:31:59.263: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.o] ** Message: 19:31:59.263: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.o ** Message: 19:31:59.270: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint] ** Message: 19:31:59.270: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.o] ** Message: 19:31:59.270: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.o ** Message: 19:31:59.276: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation] ** Message: 19:31:59.277: Processing model [a:l] ** Message: 19:31:59.277: Bootstrapper processing model [affine:local:dna2dna] ** Message: 19:31:59.277: Process optimal [optimal:affine:local:dna2dna] ** Message: 19:31:59.277: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.c ** Message: 19:31:59.693: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.c ** Message: 19:32:00.113: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.c ** Message: 19:32:00.460: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.c ** Message: 19:32:00.992: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 19:32:01.526: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.o] ** Message: 19:32:01.526: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.o ** Message: 19:32:01.531: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_score] ** Message: 19:32:01.531: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.o] ** Message: 19:32:01.531: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.o ** Message: 19:32:01.536: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_path] ** Message: 19:32:01.536: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.o] ** Message: 19:32:01.536: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.o ** Message: 19:32:01.541: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_region] ** Message: 19:32:01.541: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o] ** Message: 19:32:01.541: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o ** Message: 19:32:01.546: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint] ** Message: 19:32:01.546: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 19:32:01.546: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 19:32:01.551: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation] ** Message: 19:32:01.552: Process optimal [Terminal [Segment("START"->"match"):[affine:local:dna2dna]]] ** Message: 19:32:01.553: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.c ** Message: 19:32:02.185: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.c ** Message: 19:32:02.797: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] ** Message: 19:32:02.797: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o ** Message: 19:32:02.804: 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: 19:32:02.804: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 19:32:02.804: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 19:32:02.810: 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: 19:32:02.810: Process optimal [Terminal [Segment("match"->"END"):[affine:local:dna2dna]]] ** Message: 19:32:02.811: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.c ** Message: 19:32:03.370: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.c ** Message: 19:32:03.903: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] ** Message: 19:32:03.903: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o ** Message: 19:32:03.910: 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: 19:32:03.910: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 19:32:03.910: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 19:32:03.917: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path] ** Message: 19:32:03.917: Process optimal [HeuristicJoin:[Segment("match"->"match"):[affine:local:dna2dna]]] ** Message: 19:32:03.919: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.c ** Message: 19:32:04.877: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.c ** Message: 19:32:05.756: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] ** Message: 19:32:05.756: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o ** Message: 19:32:05.763: 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: 19:32:05.763: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 19:32:05.763: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 19:32:05.771: 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: 19:32:05.771: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.c ** Message: 19:32:06.115: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.c ** Message: 19:32:06.500: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.o] ** Message: 19:32:06.500: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.o ** Message: 19:32:06.509: Adding function [Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded] ** Message: 19:32:06.509: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.o] ** Message: 19:32:06.509: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.o ** Message: 19:32:06.517: Adding function [Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded] ** Message: 19:32:06.518: Bootstrapper processing model [affine:local:protein2protein] ** Message: 19:32:06.518: Process optimal [optimal:affine:local:protein2protein] ** Message: 19:32:06.518: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.c ** Message: 19:32:07.297: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.c ** Message: 19:32:08.613: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.c ** Message: 19:32:09.336: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.c ** Message: 19:32:09.987: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.c ** Message: 19:32:11.729: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.o] ** Message: 19:32:11.730: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.o ** Message: 19:32:11.738: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_score] ** Message: 19:32:11.738: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.o] ** Message: 19:32:11.738: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.o ** Message: 19:32:11.746: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_path] ** Message: 19:32:11.746: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.o] ** Message: 19:32:11.746: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.o ** Message: 19:32:11.754: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_region] ** Message: 19:32:11.754: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o] ** Message: 19:32:11.754: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o ** Message: 19:32:11.762: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint] ** Message: 19:32:11.762: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o] ** Message: 19:32:11.762: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o ** Message: 19:32:11.770: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation] ** Message: 19:32:11.772: Process optimal [Terminal [Segment("START"->"match"):[affine:local:protein2protein]]] ** Message: 19:32:11.774: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.c ** Message: 19:32:12.952: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.c ** Message: 19:32:14.146: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] ** Message: 19:32:14.241: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o ** Message: 19:32:14.454: 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: 19:32:14.454: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 19:32:14.454: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 19:32:14.635: 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: 19:32:14.635: Process optimal [Terminal [Segment("match"->"END"):[affine:local:protein2protein]]] ** Message: 19:32:14.636: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.c ** Message: 19:32:15.522: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.c ** Message: 19:32:16.398: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] ** Message: 19:32:16.493: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o ** Message: 19:32:16.524: 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: 19:32:16.525: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 19:32:16.525: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 19:32:16.548: 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: 19:32:16.548: Process optimal [HeuristicJoin:[Segment("match"->"match"):[affine:local:protein2protein]]] ** Message: 19:32:16.549: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.c ** Message: 19:32:17.660: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.c ** Message: 19:32:19.391: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] ** Message: 19:32:19.485: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o ** Message: 19:32:19.579: 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: 19:32:19.580: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 19:32:19.580: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 19:32:19.831: 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: 19:32:19.832: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.c ** Message: 19:32:21.714: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.c ** Message: 19:32:23.556: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.o] ** Message: 19:32:23.650: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.o ** Message: 19:32:23.839: Adding function [Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded] ** Message: 19:32:23.839: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.o] ** Message: 19:32:23.839: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.o ** Message: 19:32:23.965: Adding function [Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded] ** Message: 19:32:23.965: Processing model [a:o] ** Message: 19:32:23.966: Bootstrapper processing model [affine:overlap:dna2dna] ** Message: 19:32:23.966: Process optimal [optimal:affine:overlap:dna2dna] ** Message: 19:32:23.967: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.c ** Message: 19:32:26.391: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.c ** Message: 19:32:28.360: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.c ** Message: 19:32:29.882: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.c ** Message: 19:32:32.265: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 19:32:34.957: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.o] ** Message: 19:32:34.959: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.o ** Message: 19:32:35.123: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score] ** Message: 19:32:35.123: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.o] ** Message: 19:32:35.123: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.o ** Message: 19:32:35.343: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path] ** Message: 19:32:35.343: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.o] ** Message: 19:32:35.343: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.o ** Message: 19:32:35.587: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region] ** Message: 19:32:35.587: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.o] ** Message: 19:32:35.587: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.o ** Message: 19:32:35.863: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint] ** Message: 19:32:35.863: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 19:32:35.863: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 19:32:35.950: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation] ** Message: 19:32:35.950: Processing model [e2g] ** Message: 19:32:35.951: Bootstrapper processing model [est2genome] ** Message: 19:32:35.951: Process optimal [optimal:est2genome] ** Message: 19:32:35.953: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_est2genome_32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_est2genome_32_find_32_score.c ** Message: 19:32:37.833: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_est2genome_32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_est2genome_32_find_32_path.c ** Message: 19:32:39.825: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_est2genome_32_find_32_region.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_est2genome_32_find_32_region.c ** Message: 19:32:42.151: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_est2genome_32_find_32_checkpoint.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_est2genome_32_find_32_checkpoint.c ** Message: 19:32:47.056: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_est2genome_32_find_32_path_32_continuation.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_est2genome_32_find_32_path_32_continuation.c ** Message: 19:32:51.367: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_est2genome_32_find_32_score.o] ** Message: 19:32:51.461: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_est2genome_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_est2genome_32_find_32_score.o ** Message: 19:32:51.729: Adding function [optimal_58_est2genome_32_find_32_score] ** Message: 19:32:51.729: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_est2genome_32_find_32_path.o] ** Message: 19:32:51.729: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_est2genome_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_est2genome_32_find_32_path.o ** Message: 19:32:51.824: Adding function [optimal_58_est2genome_32_find_32_path] ** Message: 19:32:51.824: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_est2genome_32_find_32_region.o] ** Message: 19:32:51.824: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_est2genome_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_est2genome_32_find_32_region.o ** Message: 19:32:52.013: Adding function [optimal_58_est2genome_32_find_32_region] ** Message: 19:32:52.013: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_est2genome_32_find_32_checkpoint.o] ** Message: 19:32:52.013: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_est2genome_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_est2genome_32_find_32_checkpoint.o ** Message: 19:32:52.186: Adding function [optimal_58_est2genome_32_find_32_checkpoint] ** Message: 19:32:52.186: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_est2genome_32_find_32_path_32_continuation.o] ** Message: 19:32:52.186: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_est2genome_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_est2genome_32_find_32_path_32_continuation.o ** Message: 19:32:52.674: Adding function [optimal_58_est2genome_32_find_32_path_32_continuation] ** Message: 19:32:52.733: Process optimal [Terminal [Segment("START"->"match reverse"):[est2genome]]] ** Message: 19:32:52.737: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 19:32:54.779: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 19:32:56.855: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 19:32:56.885: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 19:32:57.139: 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: 19:32:57.139: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 19:32:57.139: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 19:32:57.367: 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: 19:32:57.367: Process optimal [Terminal [Segment("match reverse"->"END"):[est2genome]]] ** Message: 19:32:57.368: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 19:32:59.313: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 19:33:02.461: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 19:33:02.556: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 19:33:02.737: 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: 19:33:02.737: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 19:33:02.737: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 19:33:02.965: 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: 19:33:02.965: Process optimal [Terminal [Segment("START"->"match forward"):[est2genome]]] ** Message: 19:33:02.967: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 19:33:05.551: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 19:33:09.603: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 19:33:09.698: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 19:33:09.950: 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: 19:33:09.950: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 19:33:09.950: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 19:33:10.162: 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: 19:33:10.163: Process optimal [Terminal [Segment("match forward"->"END"):[est2genome]]] ** Message: 19:33:10.165: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 19:33:11.752: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 19:33:14.572: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 19:33:14.666: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 19:33:14.989: 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: 19:33:15.083: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 19:33:15.084: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 19:33:15.194: 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: 19:33:15.194: Process optimal [HeuristicJoin:[Segment("match reverse"->"match reverse"):[est2genome]]] ** Message: 19:33:15.201: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 19:33:19.821: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 19:33:24.501: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 19:33:24.595: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 19:33:24.745: 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: 19:33:24.745: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 19:33:24.745: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 19:33:25.004: 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: 19:33:25.004: Process optimal [Src span [Segment("match reverse"->"intron reverse"):[est2genome]]] ** Message: 19:33:25.006: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 19:33:27.179: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 19:33:30.005: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 19:33:30.099: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 19:33:30.288: 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: 19:33:30.288: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 19:33:30.288: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 19:33:30.469: 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: 19:33:30.469: Process optimal [Src span traceback [Segment("match reverse"->"intron reverse"):[est2genome]]] ** Message: 19:33:30.479: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 19:33:34.958: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 19:33:35.052: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 19:33:35.257: 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: 19:33:35.257: Process optimal [Dst span [Segment("intron reverse"->"match reverse"):[est2genome]]] ** Message: 19:33:35.259: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 19:33:38.143: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 19:33:42.572: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 19:33:42.666: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 19:33:42.808: 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: 19:33:42.808: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 19:33:42.808: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 19:33:43.034: 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: 19:33:43.034: Process optimal [HeuristicJoin:[Segment("match forward"->"match forward"):[est2genome]]] ** Message: 19:33:43.038: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 19:33:46.412: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 19:33:49.083: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 19:33:49.146: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 19:33:49.296: 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: 19:33:49.296: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 19:33:49.296: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 19:33:49.524: 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: 19:33:49.524: Process optimal [Src span [Segment("match forward"->"intron forward"):[est2genome]]] ** Message: 19:33:49.525: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 19:33:51.405: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 19:33:52.768: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 19:33:52.768: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 19:33:52.780: 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: 19:33:52.780: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 19:33:52.780: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 19:33:52.810: 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: 19:33:52.810: Process optimal [Src span traceback [Segment("match forward"->"intron forward"):[est2genome]]] ** Message: 19:33:52.814: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 19:33:55.196: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 19:33:55.196: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 19:33:55.213: 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: 19:33:55.213: Process optimal [Dst span [Segment("intron forward"->"match forward"):[est2genome]]] ** Message: 19:33:55.216: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 19:33:56.705: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 19:33:57.901: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 19:33:57.901: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 19:33:57.908: 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: 19:33:57.908: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 19:33:57.908: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 19:33:57.917: 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: 19:33:57.918: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.c ** Message: 19:33:58.339: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.c ** Message: 19:33:58.729: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.o] ** Message: 19:33:58.729: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.o ** Message: 19:33:58.736: Adding function [Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary] ** Message: 19:33:58.736: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.o] ** Message: 19:33:58.736: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.o ** Message: 19:33:58.743: Adding function [Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary] ** Message: 19:33:58.743: Processing model [ner] ** Message: 19:33:58.743: Bootstrapper processing model [NER:affine:local:dna2dna] ** Message: 19:33:58.743: Process optimal [optimal:NER:affine:local:dna2dna] ** Message: 19:33:58.744: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.c ** Message: 19:33:59.112: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.c ** Message: 19:33:59.457: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.c ** Message: 19:33:59.753: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.c ** Message: 19:34:00.192: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 19:34:00.741: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.o] ** Message: 19:34:00.741: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.o ** Message: 19:34:00.749: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score] ** Message: 19:34:00.749: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.o] ** Message: 19:34:00.749: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.o ** Message: 19:34:00.756: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path] ** Message: 19:34:00.756: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.o] ** Message: 19:34:00.756: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.o ** Message: 19:34:00.762: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region] ** Message: 19:34:00.762: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o] ** Message: 19:34:00.762: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o ** Message: 19:34:00.769: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint] ** Message: 19:34:00.769: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 19:34:00.769: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 19:34:00.777: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation] ** Message: 19:34:00.780: Process optimal [Terminal [Segment("START"->"match"):[NER:affine:local:dna2dna]]] ** Message: 19:34:00.781: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.c ** Message: 19:34:01.291: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.c ** Message: 19:34:02.107: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] ** Message: 19:34:02.108: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o ** Message: 19:34:02.119: 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: 19:34:02.119: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 19:34:02.119: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 19:34:02.129: 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: 19:34:02.129: Process optimal [Terminal [Segment("match"->"END"):[NER:affine:local:dna2dna]]] ** Message: 19:34:02.130: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.c ** Message: 19:34:02.617: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.c ** Message: 19:34:03.027: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] ** Message: 19:34:03.027: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o ** Message: 19:34:03.034: 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: 19:34:03.034: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 19:34:03.034: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 19:34:03.041: 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: 19:34:03.041: Process optimal [HeuristicJoin:[Segment("match"->"match"):[NER:affine:local:dna2dna]]] ** Message: 19:34:03.044: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.c ** Message: 19:34:03.888: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.c ** Message: 19:34:04.848: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] ** Message: 19:34:04.849: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o ** Message: 19:34:04.855: 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: 19:34:04.855: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 19:34:04.855: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 19:34:04.862: 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: 19:34:04.862: Process optimal [Src span [Segment("match"->"ner"):[NER:affine:local:dna2dna]]] ** Message: 19:34:04.863: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.c ** Message: 19:34:05.480: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.c ** Message: 19:34:05.883: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] ** Message: 19:34:05.884: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o ** Message: 19:34:05.890: 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: 19:34:05.890: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 19:34:05.890: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 19:34:05.897: 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: 19:34:05.898: Process optimal [Src span traceback [Segment("match"->"ner"):[NER:affine:local:dna2dna]]] ** Message: 19:34:05.899: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.c ** Message: 19:34:07.412: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 19:34:07.412: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 19:34:07.420: 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: 19:34:07.420: Process optimal [Dst span [Segment("ner"->"match"):[NER:affine:local:dna2dna]]] ** Message: 19:34:07.421: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.c ** Message: 19:34:07.970: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.c ** Message: 19:34:08.902: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] ** Message: 19:34:08.902: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o ** Message: 19:34:08.911: 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: 19:34:08.911: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 19:34:08.911: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 19:34:08.920: 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: 19:34:08.921: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.c ** Message: 19:34:09.236: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.c ** Message: 19:34:09.599: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.o] ** Message: 19:34:09.599: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.o ** Message: 19:34:09.606: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary] ** Message: 19:34:09.606: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.o] ** Message: 19:34:09.606: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.o ** Message: 19:34:09.614: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary] ** Message: 19:34:09.614: Bootstrapper processing model [NER:affine:local:protein2protein] ** Message: 19:34:09.614: Process optimal [optimal:NER:affine:local:protein2protein] ** Message: 19:34:09.615: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.c ** Message: 19:34:09.874: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.c ** Message: 19:34:10.195: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.c ** Message: 19:34:10.513: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.c ** Message: 19:34:11.084: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.c ** Message: 19:34:11.574: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.o] ** Message: 19:34:11.574: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.o ** Message: 19:34:11.583: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score] ** Message: 19:34:11.583: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.o] ** Message: 19:34:11.583: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.o ** Message: 19:34:11.592: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path] ** Message: 19:34:11.592: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.o] ** Message: 19:34:11.592: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.o ** Message: 19:34:11.601: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region] ** Message: 19:34:11.601: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o] ** Message: 19:34:11.601: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o ** Message: 19:34:11.611: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint] ** Message: 19:34:11.611: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o] ** Message: 19:34:11.611: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o ** Message: 19:34:11.620: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation] ** Message: 19:34:11.622: Process optimal [Terminal [Segment("START"->"match"):[NER:affine:local:protein2protein]]] ** Message: 19:34:11.623: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.c ** Message: 19:34:12.037: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.c ** Message: 19:34:12.594: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] ** Message: 19:34:12.594: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o ** Message: 19:34:12.602: 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: 19:34:12.603: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 19:34:12.603: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 19:34:12.611: 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: 19:34:12.611: Process optimal [Terminal [Segment("match"->"END"):[NER:affine:local:protein2protein]]] ** Message: 19:34:12.612: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.c ** Message: 19:34:13.058: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.c ** Message: 19:34:13.580: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] ** Message: 19:34:13.580: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o ** Message: 19:34:13.588: 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: 19:34:13.588: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 19:34:13.588: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 19:34:13.597: 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: 19:34:13.597: Process optimal [HeuristicJoin:[Segment("match"->"match"):[NER:affine:local:protein2protein]]] ** Message: 19:34:13.598: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.c ** Message: 19:34:14.318: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.c ** Message: 19:34:15.225: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] ** Message: 19:34:15.225: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o ** Message: 19:34:15.233: 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: 19:34:15.233: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 19:34:15.233: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 19:34:15.240: 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: 19:34:15.240: Process optimal [Src span [Segment("match"->"ner"):[NER:affine:local:protein2protein]]] ** Message: 19:34:15.241: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.c ** Message: 19:34:15.675: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.c ** Message: 19:34:16.061: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] ** Message: 19:34:16.061: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o ** Message: 19:34:16.067: 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: 19:34:16.067: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 19:34:16.067: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 19:34:16.074: 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: 19:34:16.074: Process optimal [Src span traceback [Segment("match"->"ner"):[NER:affine:local:protein2protein]]] ** Message: 19:34:16.076: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.c ** Message: 19:34:16.802: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 19:34:16.803: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 19:34:16.810: 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: 19:34:16.810: Process optimal [Dst span [Segment("ner"->"match"):[NER:affine:local:protein2protein]]] ** Message: 19:34:16.811: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.c ** Message: 19:34:17.210: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.c ** Message: 19:34:17.673: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] ** Message: 19:34:17.673: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o ** Message: 19:34:17.679: 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: 19:34:17.679: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 19:34:17.679: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 19:34:17.686: 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: 19:34:17.686: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.c ** Message: 19:34:17.917: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.c ** Message: 19:34:18.173: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.o] ** Message: 19:34:18.173: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.o ** Message: 19:34:18.180: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary] ** Message: 19:34:18.180: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.o] ** Message: 19:34:18.180: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.o ** Message: 19:34:18.187: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary] ** Message: 19:34:18.187: Processing model [p2d] ** Message: 19:34:18.187: Bootstrapper processing model [protein2dna:local] ** Message: 19:34:18.187: Process optimal [optimal:protein2dna:local] ** Message: 19:34:18.188: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2dna_58_local_32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2dna_58_local_32_find_32_score.c ** Message: 19:34:18.502: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2dna_58_local_32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2dna_58_local_32_find_32_path.c ** Message: 19:34:18.846: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2dna_58_local_32_find_32_region.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2dna_58_local_32_find_32_region.c ** Message: 19:34:19.204: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2dna_58_local_32_find_32_checkpoint.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2dna_58_local_32_find_32_checkpoint.c ** Message: 19:34:19.811: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.c ** Message: 19:34:20.404: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2dna_58_local_32_find_32_score.o] ** Message: 19:34:20.404: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2dna_58_local_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2dna_58_local_32_find_32_score.o ** Message: 19:34:20.411: Adding function [optimal_58_protein2dna_58_local_32_find_32_score] ** Message: 19:34:20.411: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2dna_58_local_32_find_32_path.o] ** Message: 19:34:20.411: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2dna_58_local_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2dna_58_local_32_find_32_path.o ** Message: 19:34:20.418: Adding function [optimal_58_protein2dna_58_local_32_find_32_path] ** Message: 19:34:20.418: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2dna_58_local_32_find_32_region.o] ** Message: 19:34:20.418: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2dna_58_local_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2dna_58_local_32_find_32_region.o ** Message: 19:34:20.424: Adding function [optimal_58_protein2dna_58_local_32_find_32_region] ** Message: 19:34:20.424: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2dna_58_local_32_find_32_checkpoint.o] ** Message: 19:34:20.424: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2dna_58_local_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2dna_58_local_32_find_32_checkpoint.o ** Message: 19:34:20.430: Adding function [optimal_58_protein2dna_58_local_32_find_32_checkpoint] ** Message: 19:34:20.430: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.o] ** Message: 19:34:20.430: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.o ** Message: 19:34:20.436: Adding function [optimal_58_protein2dna_58_local_32_find_32_path_32_continuation] ** Message: 19:34:20.441: Process optimal [Terminal [Segment("START"->"match"):[protein2dna:local]]] ** Message: 19:34:20.442: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.c ** Message: 19:34:21.053: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.c ** Message: 19:34:21.680: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] ** Message: 19:34:21.680: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o ** Message: 19:34:21.687: 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: 19:34:21.687: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] ** Message: 19:34:21.687: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o ** Message: 19:34:21.695: 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: 19:34:21.695: Process optimal [Terminal [Segment("match"->"END"):[protein2dna:local]]] ** Message: 19:34:21.696: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.c ** Message: 19:34:22.092: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.c ** Message: 19:34:22.547: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] ** Message: 19:34:22.547: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o ** Message: 19:34:22.557: 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: 19:34:22.557: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] ** Message: 19:34:22.557: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o ** Message: 19:34:22.564: 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: 19:34:22.564: Process optimal [HeuristicJoin:[Segment("match"->"match"):[protein2dna:local]]] ** Message: 19:34:22.566: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.c ** Message: 19:34:23.398: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.c ** Message: 19:34:24.562: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] ** Message: 19:34:24.562: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o ** Message: 19:34:24.571: 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: 19:34:24.571: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] ** Message: 19:34:24.571: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o ** Message: 19:34:24.581: 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: 19:34:24.581: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.c ** Message: 19:34:25.036: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.c ** Message: 19:34:25.303: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.o] ** Message: 19:34:25.303: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.o ** Message: 19:34:25.311: Adding function [Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded] ** Message: 19:34:25.311: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.o] ** Message: 19:34:25.311: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.o ** Message: 19:34:25.319: Adding function [Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded] ** Message: 19:34:25.319: Processing model [p2d:b] ** Message: 19:34:25.319: Bootstrapper processing model [protein2dna:bestfit] ** Message: 19:34:25.319: Process optimal [optimal:protein2dna:bestfit] ** Message: 19:34:25.321: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2dna_58_bestfit_32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2dna_58_bestfit_32_find_32_score.c ** Message: 19:34:25.894: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2dna_58_bestfit_32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2dna_58_bestfit_32_find_32_path.c ** Message: 19:34:26.652: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2dna_58_bestfit_32_find_32_region.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2dna_58_bestfit_32_find_32_region.c ** Message: 19:34:27.410: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.c ** Message: 19:34:27.980: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.c ** Message: 19:34:28.621: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2dna_58_bestfit_32_find_32_score.o] ** Message: 19:34:28.621: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2dna_58_bestfit_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2dna_58_bestfit_32_find_32_score.o ** Message: 19:34:28.628: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_score] ** Message: 19:34:28.628: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2dna_58_bestfit_32_find_32_path.o] ** Message: 19:34:28.628: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2dna_58_bestfit_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2dna_58_bestfit_32_find_32_path.o ** Message: 19:34:28.635: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_path] ** Message: 19:34:28.635: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2dna_58_bestfit_32_find_32_region.o] ** Message: 19:34:28.635: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2dna_58_bestfit_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2dna_58_bestfit_32_find_32_region.o ** Message: 19:34:28.643: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_region] ** Message: 19:34:28.643: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.o] ** Message: 19:34:28.643: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.o ** Message: 19:34:28.651: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint] ** Message: 19:34:28.651: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.o] ** Message: 19:34:28.651: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.o ** Message: 19:34:28.657: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation] ** Message: 19:34:28.658: Processing model [p2g] ** Message: 19:34:28.658: Bootstrapper processing model [protein2genome:local] ** Message: 19:34:28.658: Process optimal [optimal:protein2genome:local] ** Message: 19:34:28.659: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2genome_58_local_32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2genome_58_local_32_find_32_score.c ** Message: 19:34:29.115: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2genome_58_local_32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2genome_58_local_32_find_32_path.c ** Message: 19:34:29.632: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2genome_58_local_32_find_32_region.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2genome_58_local_32_find_32_region.c ** Message: 19:34:30.208: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2genome_58_local_32_find_32_checkpoint.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2genome_58_local_32_find_32_checkpoint.c ** Message: 19:34:31.597: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.c ** Message: 19:34:34.255: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2genome_58_local_32_find_32_score.o] ** Message: 19:34:34.256: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2genome_58_local_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2genome_58_local_32_find_32_score.o ** Message: 19:34:34.296: Adding function [optimal_58_protein2genome_58_local_32_find_32_score] ** Message: 19:34:34.296: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2genome_58_local_32_find_32_path.o] ** Message: 19:34:34.296: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2genome_58_local_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2genome_58_local_32_find_32_path.o ** Message: 19:34:34.313: Adding function [optimal_58_protein2genome_58_local_32_find_32_path] ** Message: 19:34:34.314: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2genome_58_local_32_find_32_region.o] ** Message: 19:34:34.314: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2genome_58_local_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2genome_58_local_32_find_32_region.o ** Message: 19:34:34.334: Adding function [optimal_58_protein2genome_58_local_32_find_32_region] ** Message: 19:34:34.334: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2genome_58_local_32_find_32_checkpoint.o] ** Message: 19:34:34.335: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2genome_58_local_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2genome_58_local_32_find_32_checkpoint.o ** Message: 19:34:34.367: Adding function [optimal_58_protein2genome_58_local_32_find_32_checkpoint] ** Message: 19:34:34.367: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.o] ** Message: 19:34:34.367: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.o ** Message: 19:34:34.406: Adding function [optimal_58_protein2genome_58_local_32_find_32_path_32_continuation] ** Message: 19:34:34.433: Process optimal [Terminal [Segment("START"->"match"):[protein2genome:local]]] ** Message: 19:34:34.438: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 19:34:36.940: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 19:34:40.107: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 19:34:40.108: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 19:34:40.200: 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: 19:34:40.200: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 19:34:40.200: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 19:34:40.241: 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: 19:34:40.241: Process optimal [Terminal [Segment("match"->"END"):[protein2genome:local]]] ** Message: 19:34:40.244: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 19:34:42.149: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 19:34:44.086: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 19:34:44.086: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 19:34:44.105: 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: 19:34:44.105: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 19:34:44.105: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 19:34:44.125: 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: 19:34:44.125: Process optimal [HeuristicJoin:[Segment("match"->"match"):[protein2genome:local]]] ** Message: 19:34:44.133: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 19:34:49.317: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 19:34:56.145: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 19:34:56.145: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 19:34:56.225: 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: 19:34:56.225: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 19:34:56.225: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 19:34:56.262: 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: 19:34:56.263: Process optimal [Src span [Segment("match"->"intron 0:0 phase-T"):[protein2genome:local]]] ** Message: 19:34:56.269: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 19:34:58.292: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 19:35:00.154: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 19:35:00.173: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 19:35:00.225: 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: 19:35:00.225: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 19:35:00.225: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 19:35:00.243: 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: 19:35:00.243: Process optimal [Src span traceback [Segment("match"->"intron 0:0 phase-T"):[protein2genome:local]]] ** Message: 19:35:00.256: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 19:35:04.808: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 19:35:04.808: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 19:35:04.825: 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: 19:35:04.825: Process optimal [Dst span [Segment("intron 0:0 phase-T"->"match"):[protein2genome:local]]] ** Message: 19:35:04.830: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 19:35:07.345: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 19:35:11.391: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 19:35:11.391: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 19:35:11.407: 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: 19:35:11.407: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 19:35:11.407: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 19:35:11.451: 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: 19:35:11.452: Process optimal [Src span [Segment("match"->"intron 1:2 phase-T"):[protein2genome:local]]] ** Message: 19:35:11.455: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 19:35:13.098: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 19:35:15.765: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 19:35:15.765: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 19:35:15.784: 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: 19:35:15.784: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 19:35:15.784: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 19:35:15.981: 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: 19:35:15.981: Process optimal [Src span traceback [Segment("match"->"intron 1:2 phase-T"):[protein2genome:local]]] ** Message: 19:35:15.990: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 19:35:21.449: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 19:35:21.534: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 19:35:21.579: 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: 19:35:21.580: Process optimal [Dst span [Segment("intron 1:2 phase-T"->"match"):[protein2genome:local]]] ** Message: 19:35:21.585: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 19:35:24.964: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 19:35:28.726: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 19:35:28.726: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 19:35:28.910: 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: 19:35:28.910: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 19:35:28.910: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 19:35:29.060: 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: 19:35:29.060: Process optimal [Src span [Segment("match"->"intron 2:1 phase-T"):[protein2genome:local]]] ** Message: 19:35:29.063: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 19:35:31.276: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 19:35:33.595: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 19:35:33.690: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 19:35:33.926: 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: 19:35:33.926: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 19:35:33.926: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 19:35:34.217: 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: 19:35:34.217: Process optimal [Src span traceback [Segment("match"->"intron 2:1 phase-T"):[protein2genome:local]]] ** Message: 19:35:34.313: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 19:35:39.596: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 19:35:39.596: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 19:35:39.894: 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: 19:35:39.975: Process optimal [Dst span [Segment("intron 2:1 phase-T"->"match"):[protein2genome:local]]] ** Message: 19:35:39.981: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 19:35:43.507: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 19:35:47.197: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 19:35:47.197: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 19:35:47.212: 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: 19:35:47.212: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 19:35:47.212: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 19:35:47.280: 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: 19:35:47.281: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.c ** Message: 19:35:48.340: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.c ** Message: 19:35:49.154: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.o] ** Message: 19:35:49.249: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.o ** Message: 19:35:49.292: Adding function [Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary] ** Message: 19:35:49.292: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.o] ** Message: 19:35:49.292: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.o ** Message: 19:35:49.391: Adding function [Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary] ** Message: 19:35:49.391: Processing model [p2g:b] ** Message: 19:35:49.391: Bootstrapper processing model [protein2genome:bestfit] ** Message: 19:35:49.391: Process optimal [optimal:protein2genome:bestfit] ** Message: 19:35:49.399: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2genome_58_bestfit_32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2genome_58_bestfit_32_find_32_score.c ** Message: 19:35:52.685: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2genome_58_bestfit_32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2genome_58_bestfit_32_find_32_path.c ** Message: 19:35:56.484: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2genome_58_bestfit_32_find_32_region.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2genome_58_bestfit_32_find_32_region.c ** Message: 19:36:00.636: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.c ** Message: 19:36:03.287: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.c ** Message: 19:36:05.782: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2genome_58_bestfit_32_find_32_score.o] ** Message: 19:36:05.782: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2genome_58_bestfit_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2genome_58_bestfit_32_find_32_score.o ** Message: 19:36:05.793: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_score] ** Message: 19:36:05.793: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2genome_58_bestfit_32_find_32_path.o] ** Message: 19:36:05.793: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2genome_58_bestfit_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2genome_58_bestfit_32_find_32_path.o ** Message: 19:36:05.806: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_path] ** Message: 19:36:05.806: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2genome_58_bestfit_32_find_32_region.o] ** Message: 19:36:05.806: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2genome_58_bestfit_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2genome_58_bestfit_32_find_32_region.o ** Message: 19:36:05.816: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_region] ** Message: 19:36:05.816: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.o] ** Message: 19:36:05.816: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.o ** Message: 19:36:05.827: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint] ** Message: 19:36:05.827: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.o] ** Message: 19:36:05.827: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.o ** Message: 19:36:05.839: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation] ** Message: 19:36:05.840: Processing model [c2c] ** Message: 19:36:05.840: Bootstrapper processing model [coding2coding] ** Message: 19:36:05.840: Process optimal [optimal:coding2coding] ** Message: 19:36:05.841: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_coding2coding_32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_coding2coding_32_find_32_score.c ** Message: 19:36:07.147: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_coding2coding_32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_coding2coding_32_find_32_path.c ** Message: 19:36:08.897: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_coding2coding_32_find_32_region.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_coding2coding_32_find_32_region.c ** Message: 19:36:10.274: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_coding2coding_32_find_32_checkpoint.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_coding2coding_32_find_32_checkpoint.c ** Message: 19:36:11.623: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_coding2coding_32_find_32_path_32_continuation.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_coding2coding_32_find_32_path_32_continuation.c ** Message: 19:36:13.178: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_coding2coding_32_find_32_score.o] ** Message: 19:36:13.178: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_coding2coding_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_coding2coding_32_find_32_score.o ** Message: 19:36:13.190: Adding function [optimal_58_coding2coding_32_find_32_score] ** Message: 19:36:13.190: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_coding2coding_32_find_32_path.o] ** Message: 19:36:13.190: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_coding2coding_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_coding2coding_32_find_32_path.o ** Message: 19:36:13.201: Adding function [optimal_58_coding2coding_32_find_32_path] ** Message: 19:36:13.201: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_coding2coding_32_find_32_region.o] ** Message: 19:36:13.201: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_coding2coding_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_coding2coding_32_find_32_region.o ** Message: 19:36:13.212: Adding function [optimal_58_coding2coding_32_find_32_region] ** Message: 19:36:13.212: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_coding2coding_32_find_32_checkpoint.o] ** Message: 19:36:13.212: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_coding2coding_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_coding2coding_32_find_32_checkpoint.o ** Message: 19:36:13.223: Adding function [optimal_58_coding2coding_32_find_32_checkpoint] ** Message: 19:36:13.223: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_coding2coding_32_find_32_path_32_continuation.o] ** Message: 19:36:13.223: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_coding2coding_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_coding2coding_32_find_32_path_32_continuation.o ** Message: 19:36:13.235: Adding function [optimal_58_coding2coding_32_find_32_path_32_continuation] ** Message: 19:36:13.252: Process optimal [Terminal [Segment("START"->"match"):[coding2coding]]] ** Message: 19:36:13.255: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.c ** Message: 19:36:14.474: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.c ** Message: 19:36:15.988: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o] ** Message: 19:36:15.988: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o ** Message: 19:36:15.997: 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: 19:36:15.997: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o] ** Message: 19:36:15.997: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o ** Message: 19:36:16.005: 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: 19:36:16.005: Process optimal [Terminal [Segment("match"->"END"):[coding2coding]]] ** Message: 19:36:16.007: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_score.c ** Message: 19:36:16.598: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_path.c ** Message: 19:36:17.333: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_score.o] ** Message: 19:36:17.333: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_score.o ** Message: 19:36:17.342: 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: 19:36:17.342: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_path.o] ** Message: 19:36:17.342: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_path.o ** Message: 19:36:17.351: 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: 19:36:17.351: Process optimal [HeuristicJoin:[Segment("match"->"match"):[coding2coding]]] ** Message: 19:36:17.356: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.c ** Message: 19:36:19.411: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.c ** Message: 19:36:22.776: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o] ** Message: 19:36:22.776: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o ** Message: 19:36:22.785: 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: 19:36:22.785: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o] ** Message: 19:36:22.785: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o ** Message: 19:36:22.795: 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: 19:36:22.795: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.c ** Message: 19:36:23.042: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.c ** Message: 19:36:23.300: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.o] ** Message: 19:36:23.300: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.o ** Message: 19:36:23.311: Adding function [Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded] ** Message: 19:36:23.311: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.o] ** Message: 19:36:23.311: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.o ** Message: 19:36:23.321: Adding function [Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded] ** Message: 19:36:23.321: Processing model [c2g] ** Message: 19:36:23.322: Bootstrapper processing model [coding2genome] ** Message: 19:36:23.322: Process optimal [optimal:coding2genome] ** Message: 19:36:23.324: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_coding2genome_32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_coding2genome_32_find_32_score.c ** Message: 19:36:24.186: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_coding2genome_32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_coding2genome_32_find_32_path.c ** Message: 19:36:25.164: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_coding2genome_32_find_32_region.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_coding2genome_32_find_32_region.c ** Message: 19:36:26.155: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_coding2genome_32_find_32_checkpoint.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_coding2genome_32_find_32_checkpoint.c ** Message: 19:36:29.421: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_coding2genome_32_find_32_path_32_continuation.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_coding2genome_32_find_32_path_32_continuation.c ** Message: 19:36:32.774: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_coding2genome_32_find_32_score.o] ** Message: 19:36:32.774: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_coding2genome_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_coding2genome_32_find_32_score.o ** Message: 19:36:32.784: Adding function [optimal_58_coding2genome_32_find_32_score] ** Message: 19:36:32.784: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_coding2genome_32_find_32_path.o] ** Message: 19:36:32.784: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_coding2genome_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_coding2genome_32_find_32_path.o ** Message: 19:36:32.794: Adding function [optimal_58_coding2genome_32_find_32_path] ** Message: 19:36:32.794: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_coding2genome_32_find_32_region.o] ** Message: 19:36:32.794: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_coding2genome_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_coding2genome_32_find_32_region.o ** Message: 19:36:32.803: Adding function [optimal_58_coding2genome_32_find_32_region] ** Message: 19:36:32.803: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_coding2genome_32_find_32_checkpoint.o] ** Message: 19:36:32.803: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_coding2genome_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_coding2genome_32_find_32_checkpoint.o ** Message: 19:36:32.814: Adding function [optimal_58_coding2genome_32_find_32_checkpoint] ** Message: 19:36:32.814: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_coding2genome_32_find_32_path_32_continuation.o] ** Message: 19:36:32.814: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_coding2genome_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_coding2genome_32_find_32_path_32_continuation.o ** Message: 19:36:32.826: Adding function [optimal_58_coding2genome_32_find_32_path_32_continuation] ** Message: 19:36:32.826: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.c ** Message: 19:36:33.128: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.c ** Message: 19:36:33.468: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.o] ** Message: 19:36:33.468: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.o ** Message: 19:36:33.480: Adding function [Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary] ** Message: 19:36:33.480: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.o] ** Message: 19:36:33.480: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.o ** Message: 19:36:33.490: Adding function [Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary] ** Message: 19:36:33.490: Processing model [cd2g] ** Message: 19:36:33.491: Bootstrapper processing model [cdna2genome] ** Message: 19:36:33.491: Process optimal [optimal:cdna2genome] ** Message: 19:36:33.496: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_cdna2genome_32_find_32_score.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_cdna2genome_32_find_32_score.c ** Message: 19:36:37.037: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_cdna2genome_32_find_32_path.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_cdna2genome_32_find_32_path.c ** Message: 19:36:41.392: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_cdna2genome_32_find_32_region.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_cdna2genome_32_find_32_region.c ** Message: 19:36:47.665: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_cdna2genome_32_find_32_checkpoint.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_cdna2genome_32_find_32_checkpoint.c ** Message: 19:36:58.901: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_cdna2genome_32_find_32_path_32_continuation.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_cdna2genome_32_find_32_path_32_continuation.c ** Message: 19:37:08.376: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_cdna2genome_32_find_32_score.o] ** Message: 19:37:08.376: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_cdna2genome_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_cdna2genome_32_find_32_score.o ** Message: 19:37:08.389: Adding function [optimal_58_cdna2genome_32_find_32_score] ** Message: 19:37:08.389: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_cdna2genome_32_find_32_path.o] ** Message: 19:37:08.389: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_cdna2genome_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_cdna2genome_32_find_32_path.o ** Message: 19:37:08.402: Adding function [optimal_58_cdna2genome_32_find_32_path] ** Message: 19:37:08.402: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_cdna2genome_32_find_32_region.o] ** Message: 19:37:08.402: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_cdna2genome_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_cdna2genome_32_find_32_region.o ** Message: 19:37:08.417: Adding function [optimal_58_cdna2genome_32_find_32_region] ** Message: 19:37:08.417: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_cdna2genome_32_find_32_checkpoint.o] ** Message: 19:37:08.417: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_cdna2genome_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_cdna2genome_32_find_32_checkpoint.o ** Message: 19:37:08.437: Adding function [optimal_58_cdna2genome_32_find_32_checkpoint] ** Message: 19:37:08.437: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_cdna2genome_32_find_32_path_32_continuation.o] ** Message: 19:37:08.437: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_cdna2genome_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/optimal_58_cdna2genome_32_find_32_path_32_continuation.o ** Message: 19:37:08.451: Adding function [optimal_58_cdna2genome_32_find_32_path_32_continuation] ** Message: 19:37:08.452: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.c ** Message: 19:37:09.119: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o -c /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.c ** Message: 19:37:09.746: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o] ** Message: 19:37:09.746: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o ** Message: 19:37:09.759: Adding function [Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary] ** Message: 19:37:09.759: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o] ** Message: 19:37:09.759: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o ** Message: 19:37:09.773: Adding function [Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary] ** Message: 19:37:09.773: Compiling with: [cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/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: 19:37:10.031: Adding: [c4_model_lookup.o] ** Message: 19:37:10.031: Adding object file [c4_model_lookup.o] to archive ar -Sq c4_model_archive.a c4_model_lookup.o ** Message: 19:37:10.044: Indexing archive [c4_model_archive.a] ranlib c4_model_archive.a ** Message: 19:37:10.057: Done ** Message: 19:37:10.057: Finished building bootstrapping components cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/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="\"amd64-portbld-freebsd13.5\"" -DSOURCE_ROOT_DIR="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I. -DUSE_COMPILED_MODELS -c ../../src/c4/viterbi.c ../../src/c4/viterbi.c:877:22: warning: equality comparison with extraneous parentheses [-Wparentheses-equality] 877 | if((macro[i] == '%')){ | ~~~~~~~~~^~~~~~ ../../src/c4/viterbi.c:877:22: note: remove extraneous parentheses around the comparison to silence this warning 877 | if((macro[i] == '%')){ | ~ ^ ~ ../../src/c4/viterbi.c:877:22: note: use '=' to turn this equality comparison into an assignment 877 | if((macro[i] == '%')){ | ^~ | = 1 warning generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/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="\"amd64-portbld-freebsd13.5\"" -DSOURCE_ROOT_DIR="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I. -DUSE_COMPILED_MODELS -c ../../src/sdp/scheduler.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"amd64-portbld-freebsd13.5\"" -DSOURCE_ROOT_DIR="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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:264:9: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] 264 | g_strup(primer_a); | ^ /usr/local/include/glib-2.0/glib/gstrfuncs.h:276:1: note: 'g_strup' has been explicitly marked deprecated here 276 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ ipcress.c:265:9: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] 265 | g_strup(primer_b); | ^ /usr/local/include/glib-2.0/glib/gstrfuncs.h:276:1: note: 'g_strup' has been explicitly marked deprecated here 276 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ 2 warnings generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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="\"amd64-portbld-freebsd13.5\"" -DSOURCE_ROOT_DIR="\"/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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:349:13: warning: Deprecated pre-processor symbol: replace with "g_string_append_printf" [-W#pragma-messages] 349 | g_string_sprintfa(str, "hspset: %d", index_hsp_set->target_id); | ^ /usr/local/include/glib-2.0/glib/gstring.h:296:51: note: expanded from macro 'g_string_sprintfa' 296 | #define g_string_sprintfa g_string_append_printf GLIB_DEPRECATED_MACRO_IN_2_26_FOR(g_string_append_printf) | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:40:46: note: expanded from macro 'GLIB_DEPRECATED_MACRO_IN_2_26_FOR' 40 | #define GLIB_DEPRECATED_MACRO_IN_2_26_FOR(f) GLIB_DEPRECATED_MACRO_FOR (f) | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1304:3: note: expanded from macro 'GLIB_DEPRECATED_MACRO_FOR' 1304 | _GLIB_GNUC_DO_PRAGMA(GCC warning G_STRINGIFY (Deprecated pre-processor symbol: replace with #f)) | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1301:33: note: expanded from macro '_GLIB_GNUC_DO_PRAGMA' 1301 | #define _GLIB_GNUC_DO_PRAGMA(x) _Pragma(G_STRINGIFY (x)) | ^ :150:6: note: expanded from here 150 | GCC warning "Deprecated pre-processor symbol: replace with \"g_string_append_printf\"" | ^ exonerate-server.c:354:17: warning: Deprecated pre-processor symbol: replace with "g_string_append_printf" [-W#pragma-messages] 354 | g_string_sprintfa(str, " %d %d %d", | ^ /usr/local/include/glib-2.0/glib/gstring.h:296:51: note: expanded from macro 'g_string_sprintfa' 296 | #define g_string_sprintfa g_string_append_printf GLIB_DEPRECATED_MACRO_IN_2_26_FOR(g_string_append_printf) | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:40:46: note: expanded from macro 'GLIB_DEPRECATED_MACRO_IN_2_26_FOR' 40 | #define GLIB_DEPRECATED_MACRO_IN_2_26_FOR(f) GLIB_DEPRECATED_MACRO_FOR (f) | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1304:3: note: expanded from macro 'GLIB_DEPRECATED_MACRO_FOR' 1304 | _GLIB_GNUC_DO_PRAGMA(GCC warning G_STRINGIFY (Deprecated pre-processor symbol: replace with #f)) | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1301:33: note: expanded from macro '_GLIB_GNUC_DO_PRAGMA' 1301 | #define _GLIB_GNUC_DO_PRAGMA(x) _Pragma(G_STRINGIFY (x)) | ^ :155:6: note: expanded from here 155 | GCC warning "Deprecated pre-processor symbol: replace with \"g_string_append_printf\"" | ^ exonerate-server.c:357:13: warning: Deprecated pre-processor symbol: replace with "g_string_append_printf" [-W#pragma-messages] 357 | g_string_sprintfa(str, "\n"); | ^ /usr/local/include/glib-2.0/glib/gstring.h:296:51: note: expanded from macro 'g_string_sprintfa' 296 | #define g_string_sprintfa g_string_append_printf GLIB_DEPRECATED_MACRO_IN_2_26_FOR(g_string_append_printf) | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:40:46: note: expanded from macro 'GLIB_DEPRECATED_MACRO_IN_2_26_FOR' 40 | #define GLIB_DEPRECATED_MACRO_IN_2_26_FOR(f) GLIB_DEPRECATED_MACRO_FOR (f) | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1304:3: note: expanded from macro 'GLIB_DEPRECATED_MACRO_FOR' 1304 | _GLIB_GNUC_DO_PRAGMA(GCC warning G_STRINGIFY (Deprecated pre-processor symbol: replace with #f)) | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1301:33: note: expanded from macro '_GLIB_GNUC_DO_PRAGMA' 1301 | #define _GLIB_GNUC_DO_PRAGMA(x) _Pragma(G_STRINGIFY (x)) | ^ :160:6: note: expanded from here 160 | GCC warning "Deprecated pre-processor symbol: replace with \"g_string_append_printf\"" | ^ exonerate-server.c:655:8: warning: logical not is only applied to the left hand side of this comparison [-Wlogical-not-parentheses] 655 | if(!msg[msg_len-1] == '\n') | ^ ~~ exonerate-server.c:655:8: note: add parentheses after the '!' to evaluate the comparison first 655 | if(!msg[msg_len-1] == '\n') | ^ | ( ) exonerate-server.c:655:8: note: add parentheses around left hand side expression to silence this warning 655 | if(!msg[msg_len-1] == '\n') | ^ | ( ) exonerate-server.c:676:19: warning: format specifies type 'unsigned long long' but the argument has type 'guint64' (aka 'unsigned long') [-Wformat] 670 | " %" CUSTOM_GUINT64_FORMAT | ~~~~~~~~~~~~~~~~~~~~~~~~ 671 | " %" CUSTOM_GUINT64_FORMAT 672 | " %" CUSTOM_GUINT64_FORMAT "\n", 673 | (server->dataset->header->type & 1)?"dna":"protein", 674 | (server->dataset->header->type & (1<<1)) 675 | ?"softmasked":"unmasked", 676 | server->dataset->header->number_of_seqs, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ exonerate-server.c:677:19: warning: format specifies type 'unsigned long long' but the argument has type 'guint64' (aka 'unsigned long') [-Wformat] 671 | " %" CUSTOM_GUINT64_FORMAT | ~~~~~~~~~~~~~~~~~~~~~~~~ 672 | " %" CUSTOM_GUINT64_FORMAT "\n", 673 | (server->dataset->header->type & 1)?"dna":"protein", 674 | (server->dataset->header->type & (1<<1)) 675 | ?"softmasked":"unmasked", 676 | server->dataset->header->number_of_seqs, 677 | server->dataset->header->max_seq_len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ exonerate-server.c:678:19: warning: format specifies type 'unsigned long long' but the argument has type 'guint64' (aka 'unsigned long') [-Wformat] 672 | " %" CUSTOM_GUINT64_FORMAT "\n", | ~~~~~~~~~~~~~~~~~~~~~~~~ 673 | (server->dataset->header->type & 1)?"dna":"protein", 674 | (server->dataset->header->type & (1<<1)) 675 | ?"softmasked":"unmasked", 676 | server->dataset->header->number_of_seqs, 677 | server->dataset->header->max_seq_len, 678 | server->dataset->header->total_seq_len); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ exonerate-server.c:655:24: warning: result of comparison of constant 10 with boolean expression is always false [-Wtautological-constant-out-of-range-compare] 655 | if(!msg[msg_len-1] == '\n') | ~~~~~~~~~~~~~~~ ^ ~~~~ 8 warnings generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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:70:20: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 70 | comp = g_strcasecmp; | ^ /usr/local/include/glib-2.0/glib/gstrfuncs.h:267:1: note: 'g_strcasecmp' has been explicitly marked deprecated here 267 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ 1 warning generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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:121:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 121 | if(!g_strcasecmp(query, "stdin")){ | ^ /usr/local/include/glib-2.0/glib/gstrfuncs.h:267:1: note: 'g_strcasecmp' has been explicitly marked deprecated here 267 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ 1 warning generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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:73:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 73 | if(!g_strcasecmp(remove_path, "stdin")){ | ^ /usr/local/include/glib-2.0/glib/gstrfuncs.h:267:1: note: 'g_strcasecmp' has been explicitly marked deprecated here 267 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ 1 warning generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 fastasoftmask.c:67:36: warning: self-comparison always evaluates to false [-Wtautological-compare] 67 | if(fdbs_unmasked->seq->len != fdbs_unmasked->seq->len) | ^ 1 warning generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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:130:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 130 | if(!g_strcasecmp(sort_key, "id")) | ^ /usr/local/include/glib-2.0/glib/gstrfuncs.h:267:1: note: 'g_strcasecmp' has been explicitly marked deprecated here 267 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ fastasort.c:132:14: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 132 | else if(!g_strcasecmp(sort_key, "len")) | ^ /usr/local/include/glib-2.0/glib/gstrfuncs.h:267:1: note: 'g_strcasecmp' has been explicitly marked deprecated here 267 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ fastasort.c:134:14: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 134 | else if(!g_strcasecmp(sort_key, "seq")) | ^ /usr/local/include/glib-2.0/glib/gstrfuncs.h:267:1: note: 'g_strcasecmp' has been explicitly marked deprecated here 267 | GLIB_DEPRECATED | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' 30 | #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1267:37: note: expanded from macro 'G_DEPRECATED' 1267 | #define G_DEPRECATED __attribute__((__deprecated__)) | ^ 3 warnings generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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:92:42: warning: 'g_basename' is deprecated: Use 'g_path_get_basename' instead [-Wdeprecated-declarations] 92 | output_dir, G_DIR_SEPARATOR, g_basename(query_path)); | ^ /usr/local/include/glib-2.0/glib/gfileutils.h:206:1: note: 'g_basename' has been explicitly marked deprecated here 206 | GLIB_DEPRECATED_FOR(g_path_get_basename) | ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:31:32: note: expanded from macro 'GLIB_DEPRECATED_FOR' 31 | #define GLIB_DEPRECATED_FOR(f) G_DEPRECATED_FOR(f) _GLIB_EXTERN | ^ /usr/local/include/glib-2.0/glib/gmacros.h:1277:44: note: expanded from macro 'G_DEPRECATED_FOR' 1277 | #define G_DEPRECATED_FOR(f) __attribute__((__deprecated__("Use '" #f "' instead"))) | ^ 1 warning generated. cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -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 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for exonerate-2.4.0_1 ===> Generating temporary packing list Making install in doc Making install in man Making install in man1 /usr/bin/make install-man1 /bin/sh ../../../mkinstalldirs /wrkdirs/usr/ports/biology/exonerate/work/stage/usr/local/share/man/man1 install -m 0644 ./exonerate.1 /wrkdirs/usr/ports/biology/exonerate/work/stage/usr/local/share/man/man1/exonerate.1 install -m 0644 ./ipcress.1 /wrkdirs/usr/ports/biology/exonerate/work/stage/usr/local/share/man/man1/ipcress.1 install -m 0644 ./exonerate-server.1 /wrkdirs/usr/ports/biology/exonerate/work/stage/usr/local/share/man/man1/exonerate-server.1 install -m 0644 ./fastautils.1 /wrkdirs/usr/ports/biology/exonerate/work/stage/usr/local/share/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 /wrkdirs/usr/ports/biology/exonerate/work/stage/usr/local/bin install -s -m 555 exonerate /wrkdirs/usr/ports/biology/exonerate/work/stage/usr/local/bin/exonerate install -s -m 555 ipcress /wrkdirs/usr/ports/biology/exonerate/work/stage/usr/local/bin/ipcress install -s -m 555 exonerate-server /wrkdirs/usr/ports/biology/exonerate/work/stage/usr/local/bin/exonerate-server Making install in util /bin/sh ../../mkinstalldirs /wrkdirs/usr/ports/biology/exonerate/work/stage/usr/local/bin install -s -m 555 fastaclean /wrkdirs/usr/ports/biology/exonerate/work/stage/usr/local/bin/fastaclean install -s -m 555 fastaclip /wrkdirs/usr/ports/biology/exonerate/work/stage/usr/local/bin/fastaclip install -s -m 555 fastachecksum /wrkdirs/usr/ports/biology/exonerate/work/stage/usr/local/bin/fastachecksum install -s -m 555 fastacomposition /wrkdirs/usr/ports/biology/exonerate/work/stage/usr/local/bin/fastacomposition install -s -m 555 fastadiff /wrkdirs/usr/ports/biology/exonerate/work/stage/usr/local/bin/fastadiff install -s -m 555 fastaexplode /wrkdirs/usr/ports/biology/exonerate/work/stage/usr/local/bin/fastaexplode install -s -m 555 fastafetch /wrkdirs/usr/ports/biology/exonerate/work/stage/usr/local/bin/fastafetch install -s -m 555 fastahardmask /wrkdirs/usr/ports/biology/exonerate/work/stage/usr/local/bin/fastahardmask install -s -m 555 fastaindex /wrkdirs/usr/ports/biology/exonerate/work/stage/usr/local/bin/fastaindex install -s -m 555 fastalength /wrkdirs/usr/ports/biology/exonerate/work/stage/usr/local/bin/fastalength install -s -m 555 fastanrdb /wrkdirs/usr/ports/biology/exonerate/work/stage/usr/local/bin/fastanrdb install -s -m 555 fastaoverlap /wrkdirs/usr/ports/biology/exonerate/work/stage/usr/local/bin/fastaoverlap install -s -m 555 fastareformat /wrkdirs/usr/ports/biology/exonerate/work/stage/usr/local/bin/fastareformat install -s -m 555 fastaremove /wrkdirs/usr/ports/biology/exonerate/work/stage/usr/local/bin/fastaremove install -s -m 555 fastarevcomp /wrkdirs/usr/ports/biology/exonerate/work/stage/usr/local/bin/fastarevcomp install -s -m 555 fastasoftmask /wrkdirs/usr/ports/biology/exonerate/work/stage/usr/local/bin/fastasoftmask install -s -m 555 fastasort /wrkdirs/usr/ports/biology/exonerate/work/stage/usr/local/bin/fastasort install -s -m 555 fastasplit /wrkdirs/usr/ports/biology/exonerate/work/stage/usr/local/bin/fastasplit install -s -m 555 fastasubseq /wrkdirs/usr/ports/biology/exonerate/work/stage/usr/local/bin/fastasubseq install -s -m 555 fastatranslate /wrkdirs/usr/ports/biology/exonerate/work/stage/usr/local/bin/fastatranslate install -s -m 555 fastavalidcds /wrkdirs/usr/ports/biology/exonerate/work/stage/usr/local/bin/fastavalidcds install -s -m 555 fasta2esd /wrkdirs/usr/ports/biology/exonerate/work/stage/usr/local/bin/fasta2esd install -s -m 555 fastaannotatecdna /wrkdirs/usr/ports/biology/exonerate/work/stage/usr/local/bin/fastaannotatecdna install -s -m 555 esd2esi /wrkdirs/usr/ports/biology/exonerate/work/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) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2025-12-11T19:30:37+0000' 'PKG_NOTE_ports_top_git_hash=62d8b1999233' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=5152f5f9532a' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.2' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for exonerate-2.4.0_1 ===> Building exonerate-2.4.0_1 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for exonerate-2.4.0_1 build of biology/exonerate | exonerate-2.4.0_1 ended at Thu Dec 11 14:37:22 EST 2025 build time: 00:06:46