=>> Building biology/exonerate build started at Sat Jan 24 14:55:03 EST 2026 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: 076a295eb33c 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: 12 ---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/12/.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-2.5.1.pkg [pkg.DaveG.ca] Installing pkg-2.5.1... [pkg.DaveG.ca] Extracting pkg-2.5.1: .......... 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-2.84.4,2.pkg [pkg.DaveG.ca] Installing glib-2.84.4,2... [pkg.DaveG.ca] `-- Installing gettext-runtime-0.26... [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-0.26: .......... 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-8.3.3... [pkg.DaveG.ca] | | `-- Extracting readline-8.3.3: .......... done [pkg.DaveG.ca] | `-- Extracting python311-3.11.14: .......... done [pkg.DaveG.ca] `-- Extracting py311-packaging-25.0: .......... done [pkg.DaveG.ca] Extracting glib-2.84.4,2: .......... 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: 19:58:47.892: Starting building bootstrapping components ** Message: 19:58:47.893: Processing model [u] ** Message: 19:58:47.893: Bootstrapper processing model [ungapped:dna2dna] ** Message: 19:58:47.893: Process optimal [optimal:ungapped:dna2dna] ** (process:39310): WARNING **: 19:58:47.893: Creating codegen directory [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen] ** (process:39310): WARNING **: 19:58:47.894: Creating codegen directory [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen] ** (process:39310): WARNING **: 19:58:47.894: Creating codegen directory [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5] ** (process:39310): WARNING **: 19:58:47.894: Creating codegen directory [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_5] ** Message: 19:58:47.894: 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_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: 19:58:48.896: 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: 19:58:49.379: 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: 19:58:49.734: 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: 19:58:50.547: 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: 19:58:51.274: 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: 19:58:51.274: 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: 19:58:51.310: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_score] ** Message: 19:58:51.311: 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: 19:58:51.311: 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: 19:58:51.318: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_path] ** Message: 19:58:51.318: 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: 19:58:51.318: 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: 19:58:51.368: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_region] ** Message: 19:58:51.368: 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: 19:58:51.368: 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: 19:58:51.412: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint] ** Message: 19:58:51.412: 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: 19:58:51.412: 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: 19:58:51.425: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation] ** Message: 19:58:51.426: Bootstrapper processing model [ungapped:protein2protein] ** Message: 19:58:51.426: Process optimal [optimal:ungapped:protein2protein] ** Message: 19:58:51.426: 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: 19:58:52.243: 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: 19:58:53.298: 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: 19:58:54.107: 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: 19:58:54.842: 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: 19:58:55.399: 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: 19:58:55.399: 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: 19:58:55.404: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_score] ** Message: 19:58:55.404: 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: 19:58:55.404: 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: 19:58:55.412: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_path] ** Message: 19:58:55.412: 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: 19:58:55.412: 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: 19:58:55.462: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_region] ** Message: 19:58:55.462: 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: 19:58:55.462: 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: 19:58:55.518: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint] ** Message: 19:58:55.518: 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: 19:58:55.518: 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: 19:58:55.691: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation] ** Message: 19:58:55.692: Bootstrapper processing model [ungapped:dna2protein] ** Message: 19:58:55.692: Process optimal [optimal:ungapped:dna2protein] ** Message: 19:58:55.692: 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: 19:58:56.341: 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: 19:58:57.266: 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: 19:58:58.206: 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: 19:58:59.019: 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: 19:58:59.512: 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: 19:58:59.512: 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: 19:58:59.517: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_score] ** Message: 19:58:59.517: 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: 19:58:59.517: 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: 19:58:59.521: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_path] ** Message: 19:58:59.522: 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: 19:58:59.522: 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: 19:58:59.526: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_region] ** Message: 19:58:59.526: 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: 19:58:59.526: 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: 19:58:59.550: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint] ** Message: 19:58:59.550: 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: 19:58:59.550: 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: 19:58:59.560: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation] ** Message: 19:58:59.561: Bootstrapper processing model [ungapped:protein2dna] ** Message: 19:58:59.561: Process optimal [optimal:ungapped:protein2dna] ** Message: 19:58:59.561: 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: 19:59:00.077: 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: 19:59:01.344: 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: 19:59:02.739: 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: 19:59:04.179: 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/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: 19:59:04.622: 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: 19:59:04.622: 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: 19:59:04.660: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_score] ** Message: 19:59:04.660: 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: 19:59:04.660: 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: 19:59:04.850: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_path] ** Message: 19:59:04.850: 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: 19:59:04.850: 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: 19:59:04.855: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_region] ** Message: 19:59:04.855: 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: 19:59:04.855: 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: 19:59:04.860: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint] ** Message: 19:59:04.860: 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_path_32_continuation.o] ** Message: 19:59:04.860: 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_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: 19:59:04.883: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation] ** Message: 19:59:04.883: Processing model [u:t] ** Message: 19:59:04.883: Bootstrapper processing model [ungapped:codon] ** Message: 19:59:04.883: Process optimal [optimal:ungapped:codon] ** Message: 19:59:04.884: 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: 19:59:05.586: 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: 19:59:06.509: 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: 19:59:07.330: 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: 19:59:08.157: 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: 19:59:09.006: 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: 19:59:09.016: 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: 19:59:09.021: Adding function [optimal_58_ungapped_58_codon_32_find_32_score] ** Message: 19:59:09.021: 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: 19:59:09.021: 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: 19:59:09.053: Adding function [optimal_58_ungapped_58_codon_32_find_32_path] ** Message: 19:59:09.053: 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: 19:59:09.053: 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: 19:59:09.116: Adding function [optimal_58_ungapped_58_codon_32_find_32_region] ** Message: 19:59:09.116: 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: 19:59:09.116: 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: 19:59:09.124: Adding function [optimal_58_ungapped_58_codon_32_find_32_checkpoint] ** Message: 19:59:09.124: 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: 19:59:09.124: 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: 19:59:09.221: Adding function [optimal_58_ungapped_58_codon_32_find_32_path_32_continuation] ** Message: 19:59:09.221: Processing model [a:g] ** Message: 19:59:09.221: Bootstrapper processing model [affine:global:dna2dna] ** Message: 19:59:09.221: Process optimal [optimal:affine:global:dna2dna] ** Message: 19:59:09.222: 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: 19:59:10.385: 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: 19:59:11.715: 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: 19:59:12.382: 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: 19:59:13.376: 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: 19:59:13.471: 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: 19:59:13.557: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_score] ** Message: 19:59:13.557: 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: 19:59:13.557: 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: 19:59:13.588: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_path] ** Message: 19:59:13.588: 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: 19:59:13.588: 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: 19:59:13.595: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint] ** Message: 19:59:13.595: 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: 19:59:13.595: 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: 19:59:13.628: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation] ** Message: 19:59:13.629: Bootstrapper processing model [affine:global:protein2protein] ** Message: 19:59:13.629: Process optimal [optimal:affine:global:protein2protein] ** Message: 19:59:13.629: 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: 19:59:14.558: 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: 19:59:15.542: 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: 19:59:16.796: 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: 19:59:17.738: 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: 19:59:17.786: 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: 19:59:17.974: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_score] ** Message: 19:59:17.974: 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: 19:59:17.974: 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: 19:59:17.983: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_path] ** Message: 19:59:17.984: 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: 19:59:17.984: 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: 19:59:17.993: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint] ** Message: 19:59:17.993: 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: 19:59:17.993: 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: 19:59:17.999: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation] ** Message: 19:59:17.999: Processing model [a:b] ** Message: 19:59:17.999: Bootstrapper processing model [affine:bestfit:dna2dna] ** Message: 19:59:17.999: Process optimal [optimal:affine:bestfit:dna2dna] ** Message: 19:59:18.001: 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_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: 19:59:19.073: 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: 19:59:20.205: 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: 19:59:20.988: 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: 19:59:21.729: 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: 19:59:22.860: 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: 19:59:22.860: 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: 19:59:22.867: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score] ** Message: 19:59:22.867: 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: 19:59:22.867: 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: 19:59:22.876: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path] ** Message: 19:59:22.876: 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_region.o] ** Message: 19:59:22.876: 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_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: 19:59:22.883: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region] ** Message: 19:59:22.883: 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: 19:59:22.883: 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: 19:59:23.038: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint] ** Message: 19:59:23.038: 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: 19:59:23.038: 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: 19:59:23.305: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation] ** Message: 19:59:23.306: Bootstrapper processing model [affine:bestfit:protein2protein] ** Message: 19:59:23.306: Process optimal [optimal:affine:bestfit:protein2protein] ** Message: 19:59:23.307: 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: 19:59:24.629: 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: 19:59:25.598: 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/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: 19:59:26.660: 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/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: 19:59:28.110: 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: 19:59:29.424: 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: 19:59:29.518: 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: 19:59:29.762: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score] ** Message: 19:59:29.762: 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: 19:59:29.762: 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_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: 19:59:29.920: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path] ** Message: 19:59:29.920: 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: 19:59:29.920: 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: 19:59:30.077: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region] ** Message: 19:59:30.077: 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: 19:59:30.077: 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: 19:59:30.227: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint] ** Message: 19:59:30.227: 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: 19:59:30.227: 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: 19:59:30.321: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation] ** Message: 19:59:30.321: Processing model [a:l] ** Message: 19:59:30.322: Bootstrapper processing model [affine:local:dna2dna] ** Message: 19:59:30.322: Process optimal [optimal:affine:local:dna2dna] ** Message: 19:59:30.322: 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: 19:59:31.738: 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_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: 19:59:32.668: 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: 19:59:33.571: 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: 19:59:34.590: 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: 19:59:36.116: 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: 19:59:36.194: 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: 19:59:36.368: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_score] ** Message: 19:59:36.369: 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: 19:59:36.369: 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: 19:59:36.620: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_path] ** Message: 19:59:36.620: 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: 19:59:36.620: 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: 19:59:36.880: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_region] ** Message: 19:59:36.880: 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: 19:59:36.880: 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: 19:59:36.983: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint] ** Message: 19:59:36.983: 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: 19:59:36.983: 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: 19:59:37.073: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation] ** Message: 19:59:37.075: Process optimal [Terminal [Segment("START"->"match"):[affine:local:dna2dna]]] ** Message: 19:59:37.076: 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/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: 19:59:38.338: 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: 19:59:39.424: 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: 19:59:39.518: 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: 19:59:39.699: 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: 19:59:39.699: 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: 19:59:39.699: 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: 19:59:39.930: 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: 19:59:39.931: Process optimal [Terminal [Segment("match"->"END"):[affine:local:dna2dna]]] ** Message: 19:59:39.931: 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: 19:59:40.947: 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: 19:59:41.923: 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: 19:59:41.951: 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: 19:59:42.061: 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: 19:59:42.061: 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: 19:59:42.061: 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: 19:59:42.093: 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: 19:59:42.093: Process optimal [HeuristicJoin:[Segment("match"->"match"):[affine:local:dna2dna]]] ** Message: 19:59:42.095: 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: 19:59:43.662: 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: 19:59:46.376: 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: 19:59:46.471: 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: 19:59:46.857: 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: 19:59:46.951: 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: 19:59:46.951: 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: 19:59:47.080: 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: 19:59:47.081: 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: 19:59:47.555: 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: 19:59:48.093: 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: 19:59:48.187: 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: 19:59:48.276: Adding function [Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded] ** Message: 19:59:48.276: 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: 19:59:48.276: 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: 19:59:48.284: Adding function [Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded] ** Message: 19:59:48.284: Bootstrapper processing model [affine:local:protein2protein] ** Message: 19:59:48.284: Process optimal [optimal:affine:local:protein2protein] ** Message: 19:59:48.285: 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: 19:59:49.054: 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: 19:59:49.638: 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: 19:59:50.331: 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: 19:59:50.964: 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/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: 19:59:51.595: 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: 19:59:51.595: 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: 19:59:51.610: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_score] ** Message: 19:59:51.610: 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: 19:59:51.610: 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: 19:59:51.664: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_path] ** Message: 19:59:51.664: 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: 19:59:51.665: 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: 19:59:51.722: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_region] ** Message: 19:59:51.722: 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: 19:59:51.722: 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: 19:59:51.734: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint] ** Message: 19:59:51.734: 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: 19:59:51.734: 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: 19:59:51.744: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation] ** Message: 19:59:51.746: Process optimal [Terminal [Segment("START"->"match"):[affine:local:protein2protein]]] ** Message: 19:59:51.747: 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: 19:59:52.645: 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/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: 19:59:54.219: 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: 19:59:54.290: 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: 19:59:54.502: 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: 19:59:54.502: 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: 19:59:54.502: 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: 19:59:54.679: 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: 19:59:54.679: Process optimal [Terminal [Segment("match"->"END"):[affine:local:protein2protein]]] ** Message: 19:59:54.680: 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: 19:59:55.380: 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: 19:59:56.022: 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: 19:59:56.117: 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: 19:59:56.276: 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: 19:59:56.276: 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: 19:59:56.276: 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: 19:59:56.284: 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: 19:59:56.284: Process optimal [HeuristicJoin:[Segment("match"->"match"):[affine:local:protein2protein]]] ** Message: 19:59:56.286: 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: 19:59:58.050: 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/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: 20:00:00.156: 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: 20:00:00.250: 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: 20:00:00.455: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score] ** Message: 20:00:00.455: 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: 20:00:00.455: 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: 20:00:00.677: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path] ** Message: 20:00:00.678: 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: 20:00:01.873: 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: 20:00:02.912: 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: 20:00:03.006: 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: 20:00:03.101: Adding function [Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded] ** Message: 20:00:03.101: 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: 20:00:03.101: 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: 20:00:03.272: Adding function [Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded] ** Message: 20:00:03.272: Processing model [a:o] ** Message: 20:00:03.272: Bootstrapper processing model [affine:overlap:dna2dna] ** Message: 20:00:03.272: Process optimal [optimal:affine:overlap:dna2dna] ** Message: 20:00:03.273: 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: 20:00:04.369: 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: 20:00:05.653: 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: 20:00:06.673: 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: 20:00:08.944: 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: 20:00:10.203: 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: 20:00:10.217: 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: 20:00:10.463: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score] ** Message: 20:00:10.463: 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: 20:00:10.463: 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: 20:00:10.620: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path] ** Message: 20:00:10.620: 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: 20:00:10.621: 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: 20:00:10.817: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region] ** Message: 20:00:10.817: 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: 20:00:10.817: 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: 20:00:10.988: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint] ** Message: 20:00:10.988: 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: 20:00:10.989: 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: 20:00:11.062: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation] ** Message: 20:00:11.062: Processing model [e2g] ** Message: 20:00:11.063: Bootstrapper processing model [est2genome] ** Message: 20:00:11.063: Process optimal [optimal:est2genome] ** Message: 20:00:11.065: 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: 20:00:12.394: 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: 20:00:13.900: 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: 20:00:15.412: 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/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: 20:00:18.341: 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: 20:00:20.661: 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: 20:00:20.661: 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: 20:00:20.668: Adding function [optimal_58_est2genome_32_find_32_score] ** Message: 20:00:20.668: 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: 20:00:20.668: 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: 20:00:20.693: Adding function [optimal_58_est2genome_32_find_32_path] ** Message: 20:00:20.693: 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: 20:00:20.693: 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: 20:00:20.828: Adding function [optimal_58_est2genome_32_find_32_region] ** Message: 20:00:20.828: 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: 20:00:20.828: 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: 20:00:20.975: Adding function [optimal_58_est2genome_32_find_32_checkpoint] ** Message: 20:00:20.975: 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: 20:00:20.975: 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: 20:00:20.999: Adding function [optimal_58_est2genome_32_find_32_path_32_continuation] ** Message: 20:00:21.007: Process optimal [Terminal [Segment("START"->"match reverse"):[est2genome]]] ** Message: 20:00:21.009: 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/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: 20:00:22.887: 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: 20:00:24.506: 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: 20:00:24.506: 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: 20:00:24.543: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score] ** Message: 20:00:24.544: 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: 20:00:24.544: 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: 20:00:24.613: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 20:00:24.613: Process optimal [Terminal [Segment("match reverse"->"END"):[est2genome]]] ** Message: 20:00:24.614: 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: 20:00:25.811: 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_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: 20:00:26.951: 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: 20:00:26.952: 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: 20:00:26.964: Adding function [Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score] ** Message: 20:00:26.965: 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: 20:00:26.965: 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: 20:00:26.974: Adding function [Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 20:00:26.974: Process optimal [Terminal [Segment("START"->"match forward"):[est2genome]]] ** Message: 20:00:26.977: 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: 20:00:28.223: 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: 20:00:30.164: 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: 20:00:30.211: 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: 20:00:30.222: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score] ** Message: 20:00:30.222: 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: 20:00:30.222: 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: 20:00:30.266: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 20:00:30.266: Process optimal [Terminal [Segment("match forward"->"END"):[est2genome]]] ** Message: 20:00:30.268: 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: 20:00:31.389: 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: 20:00:32.443: 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: 20:00:32.443: 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: 20:00:32.451: Adding function [Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score] ** Message: 20:00:32.451: 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: 20:00:32.451: 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: 20:00:32.542: Adding function [Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 20:00:32.542: Process optimal [HeuristicJoin:[Segment("match reverse"->"match reverse"):[est2genome]]] ** Message: 20:00:32.546: 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: 20:00:34.673: 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: 20:00:37.105: 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: 20:00:37.156: 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: 20:00:37.196: Adding function [HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score] ** Message: 20:00:37.196: 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: 20:00:37.196: 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: 20:00:37.299: Adding function [HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 20:00:37.300: Process optimal [Src span [Segment("match reverse"->"intron reverse"):[est2genome]]] ** Message: 20:00:37.301: 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: 20:00:38.962: 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: 20:00:39.905: 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: 20:00:39.949: 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: 20:00:39.956: Adding function [Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score] ** Message: 20:00:39.956: 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: 20:00:39.956: 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: 20:00:40.022: Adding function [Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 20:00:40.022: Process optimal [Src span traceback [Segment("match reverse"->"intron reverse"):[est2genome]]] ** Message: 20:00:40.025: 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: 20:00:42.384: 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: 20:00:42.479: 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: 20:00:42.652: Adding function [Src_32_span_32_traceback_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 20:00:42.652: Process optimal [Dst span [Segment("intron reverse"->"match reverse"):[est2genome]]] ** Message: 20:00:42.654: 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: 20:00:44.765: 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: 20:00:46.388: 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: 20:00:46.388: 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: 20:00:46.396: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score] ** Message: 20:00:46.396: 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: 20:00:46.396: 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: 20:00:46.403: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 20:00:46.404: Process optimal [HeuristicJoin:[Segment("match forward"->"match forward"):[est2genome]]] ** Message: 20:00:46.407: 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: 20:00:48.553: 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/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: 20:00:51.368: 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: 20:00:51.463: 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: 20:00:51.698: Adding function [HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score] ** Message: 20:00:51.698: 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: 20:00:51.698: 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: 20:00:51.731: Adding function [HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 20:00:51.731: Process optimal [Src span [Segment("match forward"->"intron forward"):[est2genome]]] ** Message: 20:00:51.732: 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: 20:00:53.615: 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/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: 20:00:55.298: 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: 20:00:55.392: 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: 20:00:55.566: Adding function [Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score] ** Message: 20:00:55.566: 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: 20:00:55.566: 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: 20:00:55.597: Adding function [Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 20:00:55.597: Process optimal [Src span traceback [Segment("match forward"->"intron forward"):[est2genome]]] ** Message: 20:00:55.603: 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: 20:00:57.809: 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: 20:00:57.882: 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: 20:00:57.967: Adding function [Src_32_span_32_traceback_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 20:00:57.967: Process optimal [Dst span [Segment("intron forward"->"match forward"):[est2genome]]] ** Message: 20:00:57.970: 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_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: 20:01:00.186: 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/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: 20:01:02.518: 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: 20:01:02.527: 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: 20:01:02.636: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score] ** Message: 20:01:02.636: 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: 20:01:02.636: 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: 20:01:02.676: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 20:01:02.677: 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: 20:01:03.621: 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/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: 20:01:05.211: 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: 20:01:05.280: 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: 20:01:05.305: Adding function [Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary] ** Message: 20:01:05.306: 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: 20:01:05.306: 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: 20:01:05.416: Adding function [Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary] ** Message: 20:01:05.416: Processing model [ner] ** Message: 20:01:05.416: Bootstrapper processing model [NER:affine:local:dna2dna] ** Message: 20:01:05.416: Process optimal [optimal:NER:affine:local:dna2dna] ** Message: 20:01:05.417: 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: 20:01:06.224: 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: 20:01:07.301: 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: 20:01:08.291: 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/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: 20:01:09.803: 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: 20:01:11.345: 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: 20:01:11.407: 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: 20:01:11.438: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score] ** Message: 20:01:11.438: 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: 20:01:11.438: 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: 20:01:11.479: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path] ** Message: 20:01:11.479: 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: 20:01:11.479: 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: 20:01:11.723: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region] ** Message: 20:01:11.723: 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: 20:01:11.723: 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: 20:01:12.012: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint] ** Message: 20:01:12.012: 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: 20:01:12.012: 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: 20:01:12.123: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation] ** Message: 20:01:12.127: Process optimal [Terminal [Segment("START"->"match"):[NER:affine:local:dna2dna]]] ** Message: 20:01:12.128: 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/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: 20:01:13.299: 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: 20:01:15.046: 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: 20:01:15.061: 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: 20:01:15.077: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score] ** Message: 20:01:15.077: 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: 20:01:15.077: 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: 20:01:15.317: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path] ** Message: 20:01:15.317: Process optimal [Terminal [Segment("match"->"END"):[NER:affine:local:dna2dna]]] ** Message: 20:01:15.318: 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/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: 20:01:16.684: 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: 20:01:17.396: 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: 20:01:17.396: 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: 20:01:17.447: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score] ** Message: 20:01:17.447: 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: 20:01:17.447: 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: 20:01:17.550: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path] ** Message: 20:01:17.550: Process optimal [HeuristicJoin:[Segment("match"->"match"):[NER:affine:local:dna2dna]]] ** Message: 20:01:17.552: 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: 20:01:19.444: 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: 20:01:22.000: 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: 20:01:22.000: 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: 20:01:22.085: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score] ** Message: 20:01:22.085: 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: 20:01:22.085: 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: 20:01:22.172: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path] ** Message: 20:01:22.172: Process optimal [Src span [Segment("match"->"ner"):[NER:affine:local:dna2dna]]] ** Message: 20:01:22.173: 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: 20:01:24.291: 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/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: 20:01:25.746: 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: 20:01:25.798: 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: 20:01:26.006: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score] ** Message: 20:01:26.007: 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: 20:01:26.007: 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: 20:01:26.124: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path] ** Message: 20:01:26.124: Process optimal [Src span traceback [Segment("match"->"ner"):[NER:affine:local:dna2dna]]] ** Message: 20:01:26.127: 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: 20:01:29.351: 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: 20:01:29.384: 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: 20:01:29.455: Adding function [Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path] ** Message: 20:01:29.455: Process optimal [Dst span [Segment("ner"->"match"):[NER:affine:local:dna2dna]]] ** Message: 20:01:29.457: 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/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: 20:01:30.818: 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: 20:01:33.046: 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: 20:01:33.140: 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: 20:01:33.416: Adding function [Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score] ** Message: 20:01:33.416: 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: 20:01:33.416: 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: 20:01:33.548: Adding function [Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path] ** Message: 20:01:33.548: 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: 20:01:34.956: 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: 20:01:36.660: 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: 20:01:36.724: 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: 20:01:37.016: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary] ** Message: 20:01:37.016: 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: 20:01:37.016: 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: 20:01:37.172: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary] ** Message: 20:01:37.172: Bootstrapper processing model [NER:affine:local:protein2protein] ** Message: 20:01:37.172: Process optimal [optimal:NER:affine:local:protein2protein] ** Message: 20:01:37.173: 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: 20:01:38.826: 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/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: 20:01:40.180: 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: 20:01:41.897: 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_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: 20:01:44.322: 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: 20:01:47.573: 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: 20:01:47.668: 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: 20:01:47.746: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score] ** Message: 20:01:47.747: 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: 20:01:47.747: 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: 20:01:47.865: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path] ** Message: 20:01:47.865: 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: 20:01:47.865: 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: 20:01:47.967: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region] ** Message: 20:01:47.967: 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: 20:01:47.967: 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: 20:01:48.172: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint] ** Message: 20:01:48.172: 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: 20:01:48.172: 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: 20:01:48.381: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation] ** Message: 20:01:48.384: Process optimal [Terminal [Segment("START"->"match"):[NER:affine:local:protein2protein]]] ** Message: 20:01:48.386: 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: 20:01:49.969: 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: 20:01:52.054: 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: 20:01:52.123: 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: 20:01:52.298: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score] ** Message: 20:01:52.298: 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: 20:01:52.298: 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: 20:01:52.487: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path] ** Message: 20:01:52.487: Process optimal [Terminal [Segment("match"->"END"):[NER:affine:local:protein2protein]]] ** Message: 20:01:52.488: 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: 20:01:53.830: 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/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: 20:01:56.179: 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: 20:01:56.274: 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: 20:01:56.518: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score] ** Message: 20:01:56.613: 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: 20:01:56.613: 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: 20:01:56.825: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path] ** Message: 20:01:56.825: Process optimal [HeuristicJoin:[Segment("match"->"match"):[NER:affine:local:protein2protein]]] ** Message: 20:01:56.828: 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: 20:02:00.041: 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: 20:02:02.243: 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: 20:02:02.291: 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: 20:02:02.424: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score] ** Message: 20:02:02.424: 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: 20:02:02.424: 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: 20:02:02.494: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path] ** Message: 20:02:02.495: Process optimal [Src span [Segment("match"->"ner"):[NER:affine:local:protein2protein]]] ** Message: 20:02:02.496: 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/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: 20:02:04.893: 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: 20:02:06.116: 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: 20:02:06.180: 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: 20:02:06.479: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score] ** Message: 20:02:06.479: 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: 20:02:06.479: 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: 20:02:06.613: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path] ** Message: 20:02:06.613: Process optimal [Src span traceback [Segment("match"->"ner"):[NER:affine:local:protein2protein]]] ** Message: 20:02:06.615: 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/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: 20:02:08.904: 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: 20:02:08.912: 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: 20:02:09.124: Adding function [Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path] ** Message: 20:02:09.125: Process optimal [Dst span [Segment("ner"->"match"):[NER:affine:local:protein2protein]]] ** Message: 20:02:09.126: 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: 20:02:10.945: 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: 20:02:12.794: 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: 20:02:12.794: 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: 20:02:13.053: Adding function [Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score] ** Message: 20:02:13.054: 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: 20:02:13.054: 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: 20:02:13.266: Adding function [Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path] ** Message: 20:02:13.267: 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: 20:02:14.432: 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: 20:02:15.824: 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: 20:02:15.824: 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: 20:02:15.834: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary] ** Message: 20:02:15.834: 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: 20:02:15.834: 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: 20:02:15.927: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary] ** Message: 20:02:15.927: Processing model [p2d] ** Message: 20:02:15.928: Bootstrapper processing model [protein2dna:local] ** Message: 20:02:15.928: Process optimal [optimal:protein2dna:local] ** Message: 20:02:15.928: 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: 20:02:16.598: 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/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: 20:02:18.039: 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: 20:02:19.716: 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: 20:02:21.983: 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: 20:02:23.912: 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: 20:02:24.006: 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: 20:02:24.211: Adding function [optimal_58_protein2dna_58_local_32_find_32_score] ** Message: 20:02:24.211: 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: 20:02:24.211: 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: 20:02:24.410: Adding function [optimal_58_protein2dna_58_local_32_find_32_path] ** Message: 20:02:24.410: 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: 20:02:24.410: 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: 20:02:24.471: Adding function [optimal_58_protein2dna_58_local_32_find_32_region] ** Message: 20:02:24.471: 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: 20:02:24.471: 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: 20:02:24.660: Adding function [optimal_58_protein2dna_58_local_32_find_32_checkpoint] ** Message: 20:02:24.660: 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: 20:02:24.660: 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: 20:02:24.849: Adding function [optimal_58_protein2dna_58_local_32_find_32_path_32_continuation] ** Message: 20:02:24.855: Process optimal [Terminal [Segment("START"->"match"):[protein2dna:local]]] ** Message: 20:02:24.858: 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: 20:02:27.292: 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/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: 20:02:29.178: 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: 20:02:29.178: 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: 20:02:29.190: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score] ** Message: 20:02:29.191: 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: 20:02:29.191: 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: 20:02:29.353: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path] ** Message: 20:02:29.353: Process optimal [Terminal [Segment("match"->"END"):[protein2dna:local]]] ** Message: 20:02:29.354: 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: 20:02:31.393: 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: 20:02:32.751: 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: 20:02:32.751: 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: 20:02:32.770: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score] ** Message: 20:02:32.770: 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: 20:02:32.770: 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: 20:02:32.865: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path] ** Message: 20:02:32.866: Process optimal [HeuristicJoin:[Segment("match"->"match"):[protein2dna:local]]] ** Message: 20:02:32.869: 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: 20:02:35.420: 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: 20:02:38.420: 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: 20:02:38.420: 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: 20:02:38.447: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score] ** Message: 20:02:38.447: 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: 20:02:38.447: 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: 20:02:38.683: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path] ** Message: 20:02:38.684: 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: 20:02:39.479: 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/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: 20:02:41.006: 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: 20:02:41.067: 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: 20:02:41.305: Adding function [Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded] ** Message: 20:02:41.306: 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: 20:02:41.306: 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: 20:02:41.353: Adding function [Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded] ** Message: 20:02:41.353: Processing model [p2d:b] ** Message: 20:02:41.353: Bootstrapper processing model [protein2dna:bestfit] ** Message: 20:02:41.353: Process optimal [optimal:protein2dna:bestfit] ** Message: 20:02:41.356: 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/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: 20:02:44.238: 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: 20:02:47.946: 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: 20:02:51.025: 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: 20:02:53.024: 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: 20:02:54.801: 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: 20:02:54.880: 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: 20:02:55.053: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_score] ** Message: 20:02:55.054: 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: 20:02:55.054: 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: 20:02:55.164: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_path] ** Message: 20:02:55.164: 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: 20:02:55.164: 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: 20:02:55.361: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_region] ** Message: 20:02:55.361: 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: 20:02:55.361: 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: 20:02:55.565: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint] ** Message: 20:02:55.565: 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: 20:02:55.565: 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: 20:02:55.754: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation] ** Message: 20:02:55.802: Processing model [p2g] ** Message: 20:02:55.802: Bootstrapper processing model [protein2genome:local] ** Message: 20:02:55.802: Process optimal [optimal:protein2genome:local] ** Message: 20:02:55.804: 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: 20:02:58.265: 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_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: 20:03:00.623: 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_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: 20:03:03.552: 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: 20:03:08.696: 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/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: 20:03:14.620: 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: 20:03:14.715: 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: 20:03:14.872: Adding function [optimal_58_protein2genome_58_local_32_find_32_score] ** Message: 20:03:14.873: 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: 20:03:14.873: 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: 20:03:14.990: Adding function [optimal_58_protein2genome_58_local_32_find_32_path] ** Message: 20:03:14.991: 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: 20:03:14.991: 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: 20:03:15.266: Adding function [optimal_58_protein2genome_58_local_32_find_32_region] ** Message: 20:03:15.266: 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: 20:03:15.266: 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: 20:03:15.479: Adding function [optimal_58_protein2genome_58_local_32_find_32_checkpoint] ** Message: 20:03:15.479: 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: 20:03:15.479: 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: 20:03:15.546: Adding function [optimal_58_protein2genome_58_local_32_find_32_path_32_continuation] ** Message: 20:03:15.574: Process optimal [Terminal [Segment("START"->"match"):[protein2genome:local]]] ** Message: 20:03:15.579: 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: 20:03:19.894: 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/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: 20:03:26.510: 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: 20:03:26.605: 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: 20:03:26.841: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score] ** Message: 20:03:26.841: 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: 20:03:26.841: 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: 20:03:26.935: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] ** Message: 20:03:26.935: Process optimal [Terminal [Segment("match"->"END"):[protein2genome:local]]] ** Message: 20:03:26.938: 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: 20:03:30.206: 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: 20:03:34.321: 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: 20:03:34.416: 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: 20:03:34.620: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score] ** Message: 20:03:34.621: 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: 20:03:34.621: 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: 20:03:34.715: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] ** Message: 20:03:34.715: Process optimal [HeuristicJoin:[Segment("match"->"match"):[protein2genome:local]]] ** Message: 20:03:34.724: 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: 20:03:43.795: 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/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: 20:03:55.972: 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: 20:03:55.972: 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: 20:03:55.993: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score] ** Message: 20:03:55.993: 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: 20:03:55.993: 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: 20:03:56.013: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] ** Message: 20:03:56.013: Process optimal [Src span [Segment("match"->"intron 0:0 phase-T"):[protein2genome:local]]] ** Message: 20:03:56.016: 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: 20:03:58.949: 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: 20:04:02.731: 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: 20:04:02.825: 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: 20:04:03.018: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score] ** Message: 20:04:03.019: 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: 20:04:03.019: 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: 20:04:03.250: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] ** Message: 20:04:03.250: Process optimal [Src span traceback [Segment("match"->"intron 0:0 phase-T"):[protein2genome:local]]] ** Message: 20:04:03.354: 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: 20:04:14.030: 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: 20:04:14.093: 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: 20:04:14.258: Adding function [Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] ** Message: 20:04:14.258: Process optimal [Dst span [Segment("intron 0:0 phase-T"->"match"):[protein2genome:local]]] ** Message: 20:04:14.265: 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/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: 20:04:19.383: 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: 20:04:27.053: 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: 20:04:27.067: 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: 20:04:27.282: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score] ** Message: 20:04:27.282: 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: 20:04:27.282: 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: 20:04:27.405: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] ** Message: 20:04:27.405: Process optimal [Src span [Segment("match"->"intron 1:2 phase-T"):[protein2genome:local]]] ** Message: 20:04:27.408: 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: 20:04:30.994: 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: 20:04:36.991: 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: 20:04:37.085: 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: 20:04:37.266: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score] ** Message: 20:04:37.266: 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: 20:04:37.266: 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: 20:04:37.488: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] ** Message: 20:04:37.488: Process optimal [Src span traceback [Segment("match"->"intron 1:2 phase-T"):[protein2genome:local]]] ** Message: 20:04:37.498: 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: 20:04:48.479: 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: 20:04:48.518: 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: 20:04:48.770: Adding function [Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] ** Message: 20:04:48.770: Process optimal [Dst span [Segment("intron 1:2 phase-T"->"match"):[protein2genome:local]]] ** Message: 20:04:48.775: 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: 20:04:54.083: 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: 20:04:58.943: 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: 20:04:59.014: 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: 20:04:59.282: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score] ** Message: 20:04:59.282: 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: 20:04:59.282: 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: 20:04:59.550: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] ** Message: 20:04:59.550: Process optimal [Src span [Segment("match"->"intron 2:1 phase-T"):[protein2genome:local]]] ** Message: 20:04:59.553: 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/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: 20:05:01.813: 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: 20:05:04.594: 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: 20:05:04.594: 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: 20:05:04.611: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score] ** Message: 20:05:04.611: 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: 20:05:04.611: 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: 20:05:04.637: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] ** Message: 20:05:04.637: Process optimal [Src span traceback [Segment("match"->"intron 2:1 phase-T"):[protein2genome:local]]] ** Message: 20:05:04.646: 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: 20:05:08.857: 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: 20:05:08.951: 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: 20:05:09.172: Adding function [Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] ** Message: 20:05:09.172: Process optimal [Dst span [Segment("intron 2:1 phase-T"->"match"):[protein2genome:local]]] ** Message: 20:05:09.177: 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: 20:05:12.915: 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: 20:05:16.641: 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: 20:05:16.641: 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: 20:05:16.660: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score] ** Message: 20:05:16.660: 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: 20:05:16.660: 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: 20:05:16.737: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] ** Message: 20:05:16.738: 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/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: 20:05:18.330: 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: 20:05:19.628: 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: 20:05:19.652: 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: 20:05:19.798: Adding function [Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary] ** Message: 20:05:19.798: 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: 20:05:19.798: 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: 20:05:19.852: Adding function [Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary] ** Message: 20:05:19.853: Processing model [p2g:b] ** Message: 20:05:19.853: Bootstrapper processing model [protein2genome:bestfit] ** Message: 20:05:19.854: Process optimal [optimal:protein2genome:bestfit] ** Message: 20:05:19.860: 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: 20:05:24.828: 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: 20:05:29.673: 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: 20:05:35.815: 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: 20:05:40.500: 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: 20:05:44.494: 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: 20:05:44.589: 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: 20:05:44.779: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_score] ** Message: 20:05:44.779: 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: 20:05:44.779: 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: 20:05:44.927: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_path] ** Message: 20:05:44.928: 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: 20:05:44.928: 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: 20:05:45.158: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_region] ** Message: 20:05:45.159: 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: 20:05:45.159: 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: 20:05:45.400: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint] ** Message: 20:05:45.400: 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: 20:05:45.400: 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: 20:05:45.542: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation] ** Message: 20:05:45.542: Processing model [c2c] ** Message: 20:05:45.542: Bootstrapper processing model [coding2coding] ** Message: 20:05:45.542: Process optimal [optimal:coding2coding] ** Message: 20:05:45.544: 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: 20:05:48.350: 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: 20:05:51.048: 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: 20:05:52.760: 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: 20:05:56.486: 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: 20:06:01.998: 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: 20:06:02.043: 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: 20:06:02.164: Adding function [optimal_58_coding2coding_32_find_32_score] ** Message: 20:06:02.164: 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: 20:06:02.164: 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: 20:06:02.431: Adding function [optimal_58_coding2coding_32_find_32_path] ** Message: 20:06:02.432: 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: 20:06:02.432: 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: 20:06:02.589: Adding function [optimal_58_coding2coding_32_find_32_region] ** Message: 20:06:02.589: 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: 20:06:02.589: 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: 20:06:02.746: Adding function [optimal_58_coding2coding_32_find_32_checkpoint] ** Message: 20:06:02.747: 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: 20:06:02.747: 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: 20:06:02.838: Adding function [optimal_58_coding2coding_32_find_32_path_32_continuation] ** Message: 20:06:02.865: Process optimal [Terminal [Segment("START"->"match"):[coding2coding]]] ** Message: 20:06:02.905: 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: 20:06:07.052: 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: 20:06:12.439: 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: 20:06:12.534: 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: 20:06:12.723: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score] ** Message: 20:06:12.723: 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: 20:06:12.723: 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: 20:06:12.957: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path] ** Message: 20:06:12.957: Process optimal [Terminal [Segment("match"->"END"):[coding2coding]]] ** Message: 20:06:12.960: 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: 20:06:15.017: 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: 20:06:17.099: 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: 20:06:17.180: 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: 20:06:17.628: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_score] ** Message: 20:06:17.723: 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: 20:06:17.723: 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: 20:06:17.888: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_path] ** Message: 20:06:17.888: Process optimal [HeuristicJoin:[Segment("match"->"match"):[coding2coding]]] ** Message: 20:06:17.895: 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: 20:06:23.460: 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/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: 20:06:28.948: 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: 20:06:28.948: 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: 20:06:28.975: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score] ** Message: 20:06:28.975: 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: 20:06:28.975: 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: 20:06:29.124: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path] ** Message: 20:06:29.125: 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: 20:06:29.893: 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: 20:06:30.487: 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: 20:06:30.581: 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: 20:06:30.742: Adding function [Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded] ** Message: 20:06:30.742: 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: 20:06:30.742: 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: 20:06:30.850: Adding function [Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded] ** Message: 20:06:30.850: Processing model [c2g] ** Message: 20:06:30.851: Bootstrapper processing model [coding2genome] ** Message: 20:06:30.851: Process optimal [optimal:coding2genome] ** Message: 20:06:30.855: 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: 20:06:33.156: 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: 20:06:35.334: 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: 20:06:37.780: 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: 20:06:42.653: 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: 20:06:49.943: 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: 20:06:50.038: 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: 20:06:50.242: Adding function [optimal_58_coding2genome_32_find_32_score] ** Message: 20:06:50.243: 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: 20:06:50.243: 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: 20:06:50.620: Adding function [optimal_58_coding2genome_32_find_32_path] ** Message: 20:06:50.715: 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: 20:06:50.715: 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: 20:06:51.014: Adding function [optimal_58_coding2genome_32_find_32_region] ** Message: 20:06:51.109: 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: 20:06:51.109: 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: 20:06:51.298: Adding function [optimal_58_coding2genome_32_find_32_checkpoint] ** Message: 20:06:51.298: 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: 20:06:51.298: 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: 20:06:51.487: Adding function [optimal_58_coding2genome_32_find_32_path_32_continuation] ** Message: 20:06:51.487: 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: 20:06:52.669: 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: 20:06:53.419: 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: 20:06:53.479: 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: 20:06:53.573: Adding function [Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary] ** Message: 20:06:53.573: 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: 20:06:53.573: 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: 20:06:53.762: Adding function [Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary] ** Message: 20:06:53.762: Processing model [cd2g] ** Message: 20:06:53.764: Bootstrapper processing model [cdna2genome] ** Message: 20:06:53.764: Process optimal [optimal:cdna2genome] ** Message: 20:06:53.771: 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/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: 20:06:57.730: 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: 20:07:03.110: 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: 20:07:08.117: 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: 20:07:22.950: 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: 20:07:34.080: 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: 20:07:34.080: 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: 20:07:34.098: Adding function [optimal_58_cdna2genome_32_find_32_score] ** Message: 20:07:34.098: 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: 20:07:34.098: 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: 20:07:34.121: Adding function [optimal_58_cdna2genome_32_find_32_path] ** Message: 20:07:34.121: 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: 20:07:34.121: 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: 20:07:34.186: Adding function [optimal_58_cdna2genome_32_find_32_region] ** Message: 20:07:34.186: 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: 20:07:34.186: 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: 20:07:34.282: Adding function [optimal_58_cdna2genome_32_find_32_checkpoint] ** Message: 20:07:34.282: 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: 20:07:34.282: 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: 20:07:34.353: Adding function [optimal_58_cdna2genome_32_find_32_path_32_continuation] ** Message: 20:07:34.354: 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: 20:07:35.147: 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/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: 20:07:36.536: 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: 20:07:36.557: 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: 20:07:36.615: Adding function [Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary] ** Message: 20:07:36.615: 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: 20:07:36.615: 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: 20:07:36.636: Adding function [Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary] ** Message: 20:07:36.636: 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: 20:07:38.014: Adding: [c4_model_lookup.o] ** Message: 20:07:38.109: Adding object file [c4_model_lookup.o] to archive ar -Sq c4_model_archive.a c4_model_lookup.o ** Message: 20:07:38.376: Indexing archive [c4_model_archive.a] ranlib c4_model_archive.a ** Message: 20:07:38.502: Done ** Message: 20:07:38.502: 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=2026-01-24T19:55:03+0000' 'PKG_NOTE_ports_top_git_hash=076a295eb33c' '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 Sat Jan 24 15:09:32 EST 2026 build time: 00:14:31