=>> Building biology/exonerate build started at Wed Apr 3 17:05:54 BST 2024 port directory: /usr/ports/biology/exonerate package name: exonerate-2.4.0_1 building for: FreeBSD pkg-builder.dan.net.uk 13.2-RELEASE-p10 FreeBSD 13.2-RELEASE-p10 amd64 maintained by: mzaki@niid.go.jp Makefile datestamp: -rw-r--r-- 1 root wheel 516 Feb 25 10:26 /usr/ports/biology/exonerate/Makefile Ports top last git commit: c2c35d895e Ports top unclean checkout: yes Port dir last git commit: 2044d70d1f Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.99.20240122_1 Host OSVERSION: 1400097 Jail OSVERSION: 1302001 Job Id: 08 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1302001 UNAME_v=FreeBSD 13.2-RELEASE-p10 UNAME_r=13.2-RELEASE-p10 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 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--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=/ccache/libexec/ccache:/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 LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8 CCACHE_DIR="/root/.ccache" 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 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GTK4_VERSION="4.0.0" OSREL=13.2 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--- 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 #### #### CCACHE_CPP2=1 WITH_SSP_PORTS=yes WITH_SSP=yes #WITH_LTO=yes DISABLE_LICENSES=yes LICENSES_ACCEPTED=AGPLv3 APACHE10 APACHE11 APACHE20 ART10 ARTPERL10 ART20 BSD BSD2CLAUSE BSD3CLAUSE BSD4CLAUSE BSL CC0-1.0 CDDL ClArtistic EPL GFDL GMGPL GPLv1 GPLv2 GPLv3 GPLv3RLE ISCL LGPL20 LGPL21 LGPL3 LPPL10 LPPL11 LPPL12 LPPL13 LPPL13a LPPL13b LPPL13c MIT MPL OpenSSL OFL10 OFL11 OWL PostgreSQL PHP202 PHP30 PHP301 PSFL RUBY ZLIB ZPL21 SVM-Light EULA ALASIR Microsoft-exFAT SIMIAN UDEVGAME unknown MTA COMMERCIAL teamspeak NO_LICENSES_DIALOGS=yes #### #### NO_IGNORE=yes DEFAULT_VERSIONS+=ssl=openssl mysql=8.0 imagemagick=7 samba=4.13 java=18 WITH_SETID_MODE=force PHP_ZTS=enabled OPTIONS_UNSET+=OPENJPEG OPTIONS_UNSET+=GSSAPI_BASE OPTIONS_SET+=ZTS OPTIONS_SET+=GSSAPI_NONE WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache NO_CCACHE_DEPEND=1 CCACHE_WRAPPER_PATH= /ccache/libexec/ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---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 =========================================================================== =================================================== ===== 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-1.20.9_1.pkg [pkg-builder.dan.net.uk] Installing pkg-1.20.9_1... [pkg-builder.dan.net.uk] Extracting pkg-1.20.9_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 ===> Fetching all distfiles required by exonerate-2.4.0_1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> 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 ===> 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-2.1.1,1.pkg [pkg-builder.dan.net.uk] Installing pkgconf-2.1.1,1... [pkg-builder.dan.net.uk] Extracting pkgconf-2.1.1,1: .......... done ===> exonerate-2.4.0_1 depends on package: pkgconf>=1.3.0_1 - found ===> Returning to build of exonerate-2.4.0_1 =========================================================================== =================================================== ===== 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-2.80.0,2.pkg [pkg-builder.dan.net.uk] Installing glib-2.80.0,2... [pkg-builder.dan.net.uk] `-- Installing gettext-runtime-0.22.3_1... [pkg-builder.dan.net.uk] | `-- Installing indexinfo-0.3.1... [pkg-builder.dan.net.uk] | `-- Extracting indexinfo-0.3.1: . done [pkg-builder.dan.net.uk] `-- Extracting gettext-runtime-0.22.3_1: .......... done [pkg-builder.dan.net.uk] `-- Installing libffi-3.4.4_1... [pkg-builder.dan.net.uk] `-- Extracting libffi-3.4.4_1: .......... done [pkg-builder.dan.net.uk] `-- Installing libiconv-1.17_1... [pkg-builder.dan.net.uk] `-- Extracting libiconv-1.17_1: .......... done [pkg-builder.dan.net.uk] `-- Installing pcre2-10.43... [pkg-builder.dan.net.uk] | `-- Installing readline-8.2.10... [pkg-builder.dan.net.uk] | `-- Extracting readline-8.2.10: .......... done [pkg-builder.dan.net.uk] `-- Extracting pcre2-10.43: .......... done [pkg-builder.dan.net.uk] `-- Installing py39-packaging-23.2... [pkg-builder.dan.net.uk] | `-- Installing python39-3.9.18_1... [pkg-builder.dan.net.uk] | | `-- Installing mpdecimal-2.5.1... [pkg-builder.dan.net.uk] | | `-- Extracting mpdecimal-2.5.1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing openssl-3.0.13_1,1... [pkg-builder.dan.net.uk] | | `-- Extracting openssl-3.0.13_1,1: .......... done [pkg-builder.dan.net.uk] | `-- Extracting python39-3.9.18_1: .......... done [pkg-builder.dan.net.uk] `-- Extracting py39-packaging-23.2: .......... done [pkg-builder.dan.net.uk] Extracting glib-2.80.0,2: .......... 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 python39-3.9.18_1: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py39-gdbm databases/py-gdbm@py39 py39-sqlite3 databases/py-sqlite3@py39 py39-tkinter x11-toolkits/py-tkinter@py39 ===> 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-freebsd13.2 checking host system type... amd64-portbld-freebsd13.2 Set host to amd64-portbld-freebsd13.2 amd64-portbld-freebsd13.2 *** Unknown build platform: amd64-portbld-freebsd13.2 *** 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 -fstack-protector-strong -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 -fstack-protector-strong -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 -fstack-protector-strong -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 -fstack-protector-strong -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] 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 GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #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 -fstack-protector-strong -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] if(pow(vfsm->alphabet_size, depth) >= VFSM_MAX){ ~~ ^~~~~~~~ ./vfsm.h:24:18: note: expanded from macro 'VFSM_MAX' #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' #define G_GINT64_CONSTANT(val) (val##L) ^~~~~~ :124:1: note: expanded from here 18446744073709551615UL ^~~~~~~~~~~~~~~~~~~~~~ vfsm.c:99:12: warning: format specifies type 'unsigned long long' but the argument has type 'VFSM_Int' (aka 'unsigned long') [-Wformat] vfsm->prs, ^~~~~~~~~~ /usr/local/include/glib-2.0/glib/gmessages.h:358:32: note: expanded from macro 'g_message' __VA_ARGS__) ^~~~~~~~~~~ vfsm.c:100:12: warning: format specifies type 'unsigned long long' but the argument has type 'VFSM_Int' (aka 'unsigned long') [-Wformat] vfsm->prw, ^~~~~~~~~~ /usr/local/include/glib-2.0/glib/gmessages.h:358:32: note: expanded from macro 'g_message' __VA_ARGS__) ^~~~~~~~~~~ vfsm.c:101:12: warning: format specifies type 'unsigned long long' but the argument has type 'VFSM_Int' (aka 'unsigned long') [-Wformat] vfsm->lrs, ^~~~~~~~~~ /usr/local/include/glib-2.0/glib/gmessages.h:358:32: note: expanded from macro 'g_message' __VA_ARGS__) ^~~~~~~~~~~ vfsm.c:102:12: warning: format specifies type 'unsigned long long' but the argument has type 'VFSM_Int' (aka 'unsigned long') [-Wformat] vfsm->lrw, ^~~~~~~~~~ /usr/local/include/glib-2.0/glib/gmessages.h:358:32: note: expanded from macro 'g_message' __VA_ARGS__) ^~~~~~~~~~~ vfsm.c:103:12: warning: format specifies type 'unsigned long long' but the argument has type 'VFSM_Int' (aka 'unsigned long') [-Wformat] vfsm->total ^~~~~~~~~~~ /usr/local/include/glib-2.0/glib/gmessages.h:358:32: note: expanded from macro 'g_message' __VA_ARGS__) ^~~~~~~~~~~ vfsm.c:108:20: warning: format specifies type 'unsigned long long' but the argument has type 'VFSM_Int' (aka 'unsigned long') [-Wformat] 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 -fstack-protector-strong -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 -fstack-protector-strong -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 -fstack-protector-strong -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 -fstack-protector-strong -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 -fstack-protector-strong -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 -fstack-protector-strong -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 -fstack-protector-strong -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] 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 GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #define G_DEPRECATED __attribute__((__deprecated__)) ^ argument.c:140:13: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 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 GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #define G_DEPRECATED __attribute__((__deprecated__)) ^ argument.c:306:9: warning: Deprecated pre-processor symbol [-W#pragma-messages] if(!g_thread_supported()) ^ /usr/local/include/glib-2.0/glib/deprecated/gthread.h:280:38: note: expanded from macro 'g_thread_supported' #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' #define GLIB_DEPRECATED_MACRO_IN_2_32 GLIB_DEPRECATED_MACRO ^ /usr/local/include/glib-2.0/glib/gmacros.h:1298:31: note: expanded from macro 'GLIB_DEPRECATED_MACRO' #define GLIB_DEPRECATED_MACRO _GLIB_GNUC_DO_PRAGMA(GCC warning "Deprecated pre-processor symbol") ^ /usr/local/include/glib-2.0/glib/gmacros.h:1297:33: note: expanded from macro '_GLIB_GNUC_DO_PRAGMA' #define _GLIB_GNUC_DO_PRAGMA(x) _Pragma(G_STRINGIFY (x)) ^ :217:6: note: expanded from here GCC warning "Deprecated pre-processor symbol" ^ argument.c:307:9: warning: 'g_thread_init' is deprecated [-Wdeprecated-declarations] 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 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' #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' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #define G_DEPRECATED __attribute__((__deprecated__)) ^ argument.c:502:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] 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 GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #define G_DEPRECATED __attribute__((__deprecated__)) ^ argument.c:559:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] 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 GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #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 -fstack-protector-strong -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 -fstack-protector-strong -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 -fstack-protector-strong -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] g_string_sprintfa(full_msg, "linecount: %d\n", line_count+1); ^ /usr/local/include/glib-2.0/glib/gstring.h:292:51: note: expanded from macro 'g_string_sprintfa' #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' #define GLIB_DEPRECATED_MACRO_IN_2_26_FOR(f) GLIB_DEPRECATED_MACRO_FOR (f) ^ /usr/local/include/glib-2.0/glib/gmacros.h:1300:3: note: expanded from macro 'GLIB_DEPRECATED_MACRO_FOR' _GLIB_GNUC_DO_PRAGMA(GCC warning G_STRINGIFY (Deprecated pre-processor symbol: replace with #f)) ^ /usr/local/include/glib-2.0/glib/gmacros.h:1297:33: note: expanded from macro '_GLIB_GNUC_DO_PRAGMA' #define _GLIB_GNUC_DO_PRAGMA(x) _Pragma(G_STRINGIFY (x)) ^ :146:6: note: expanded from here 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] g_string_sprintfa(full_msg, "%s", msg); ^ /usr/local/include/glib-2.0/glib/gstring.h:292:51: note: expanded from macro 'g_string_sprintfa' #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' #define GLIB_DEPRECATED_MACRO_IN_2_26_FOR(f) GLIB_DEPRECATED_MACRO_FOR (f) ^ /usr/local/include/glib-2.0/glib/gmacros.h:1300:3: note: expanded from macro 'GLIB_DEPRECATED_MACRO_FOR' _GLIB_GNUC_DO_PRAGMA(GCC warning G_STRINGIFY (Deprecated pre-processor symbol: replace with #f)) ^ /usr/local/include/glib-2.0/glib/gmacros.h:1297:33: note: expanded from macro '_GLIB_GNUC_DO_PRAGMA' #define _GLIB_GNUC_DO_PRAGMA(x) _Pragma(G_STRINGIFY (x)) ^ :151:6: note: expanded from here 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 -fstack-protector-strong -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] if(!g_thread_supported()) ^ /usr/local/include/glib-2.0/glib/deprecated/gthread.h:280:38: note: expanded from macro 'g_thread_supported' #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' #define GLIB_DEPRECATED_MACRO_IN_2_32 GLIB_DEPRECATED_MACRO ^ /usr/local/include/glib-2.0/glib/gmacros.h:1298:31: note: expanded from macro 'GLIB_DEPRECATED_MACRO' #define GLIB_DEPRECATED_MACRO _GLIB_GNUC_DO_PRAGMA(GCC warning "Deprecated pre-processor symbol") ^ /usr/local/include/glib-2.0/glib/gmacros.h:1297:33: note: expanded from macro '_GLIB_GNUC_DO_PRAGMA' #define _GLIB_GNUC_DO_PRAGMA(x) _Pragma(G_STRINGIFY (x)) ^ :121:6: note: expanded from here GCC warning "Deprecated pre-processor symbol" ^ jobqueue.test.c:35:9: warning: 'g_thread_init' is deprecated [-Wdeprecated-declarations] 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 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' #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' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #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 -fstack-protector-strong -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 -fstack-protector-strong -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] 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 GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #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] 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 GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #define G_DEPRECATED __attribute__((__deprecated__)) ^ alphabet.c:320:13: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 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 GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #define G_DEPRECATED __attribute__((__deprecated__)) ^ alphabet.c:323:13: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 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 GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #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] 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 GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #define G_DEPRECATED __attribute__((__deprecated__)) ^ splice.c:195:40: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 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 GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #define G_DEPRECATED __attribute__((__deprecated__)) ^ splice.c:203:40: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 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 GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #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 -fstack-protector-strong -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 -fstack-protector-strong -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 -fstack-protector-strong -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 -fstack-protector-strong -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 -fstack-protector-strong -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 -fstack-protector-strong -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 -fstack-protector-strong -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] g_strdown(query_str); ^ /usr/local/include/glib-2.0/glib/gstrfuncs.h:274:1: note: 'g_strdown' has been explicitly marked deprecated here GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #define G_DEPRECATED __attribute__((__deprecated__)) ^ hspset.c:638:9: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] g_strdown(target_str); ^ /usr/local/include/glib-2.0/glib/gstrfuncs.h:274:1: note: 'g_strdown' has been explicitly marked deprecated here GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #define G_DEPRECATED __attribute__((__deprecated__)) ^ hspset.c:640:9: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] g_strup(query_str); ^ /usr/local/include/glib-2.0/glib/gstrfuncs.h:276:1: note: 'g_strup' has been explicitly marked deprecated here GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #define G_DEPRECATED __attribute__((__deprecated__)) ^ hspset.c:641:9: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] g_strup(target_str); ^ /usr/local/include/glib-2.0/glib/gstrfuncs.h:276:1: note: 'g_strup' has been explicitly marked deprecated here GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #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 -fstack-protector-strong -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] 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' #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 GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #define G_DEPRECATED __attribute__((__deprecated__)) ^ pcr.c:59:37: warning: 'g_mem_chunk_alloc' is deprecated [-Wdeprecated-declarations] 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' #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 GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #define G_DEPRECATED __attribute__((__deprecated__)) ^ pcr.c:69:5: warning: 'g_mem_chunk_free' is deprecated [-Wdeprecated-declarations] 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 GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #define G_DEPRECATED __attribute__((__deprecated__)) ^ pcr.c:155:39: warning: 'g_mem_chunk_alloc' is deprecated [-Wdeprecated-declarations] 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' #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 GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #define G_DEPRECATED __attribute__((__deprecated__)) ^ pcr.c:174:5: warning: 'g_mem_chunk_free' is deprecated [-Wdeprecated-declarations] 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 GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #define G_DEPRECATED __attribute__((__deprecated__)) ^ pcr.c:252:5: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] 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 GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #define G_DEPRECATED __attribute__((__deprecated__)) ^ pcr.c:253:5: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] 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 GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #define G_DEPRECATED __attribute__((__deprecated__)) ^ pcr.c:357:29: warning: 'g_mem_chunk_new' is deprecated [-Wdeprecated-declarations] 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 GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #define G_DEPRECATED __attribute__((__deprecated__)) ^ pcr.c:363:28: warning: 'g_mem_chunk_new' is deprecated [-Wdeprecated-declarations] 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 GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #define G_DEPRECATED __attribute__((__deprecated__)) ^ pcr.c:366:28: warning: 'g_mem_chunk_new' is deprecated [-Wdeprecated-declarations] 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 GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #define G_DEPRECATED __attribute__((__deprecated__)) ^ pcr.c:381:5: warning: 'g_mem_chunk_destroy' is deprecated [-Wdeprecated-declarations] 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 GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #define G_DEPRECATED __attribute__((__deprecated__)) ^ pcr.c:383:5: warning: 'g_mem_chunk_destroy' is deprecated [-Wdeprecated-declarations] 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 GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #define G_DEPRECATED __attribute__((__deprecated__)) ^ pcr.c:384:5: warning: 'g_mem_chunk_destroy' is deprecated [-Wdeprecated-declarations] 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 GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #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 -fstack-protector-strong -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 -fstack-protector-strong -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 -fstack-protector-strong -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] 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 GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #define G_DEPRECATED __attribute__((__deprecated__)) ^ seeder.c:273:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 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 GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #define G_DEPRECATED __attribute__((__deprecated__)) ^ seeder.c:275:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 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 GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #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 -fstack-protector-strong -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 -fstack-protector-strong -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 -fstack-protector-strong -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] 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] 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 -fstack-protector-strong -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] removed_words, removed_instances); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/include/glib-2.0/glib/gmessages.h:358:32: note: expanded from macro 'g_message' __VA_ARGS__) ^~~~~~~~~~~ index.c:379:30: warning: format specifies type 'unsigned long long' but the argument has type 'gint64' (aka 'long') [-Wformat] removed_words, removed_instances); ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /usr/local/include/glib-2.0/glib/gmessages.h:358:32: note: expanded from macro 'g_message' __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 -fstack-protector-strong -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-freebsd13.2\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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-freebsd13.2\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -fstack-protector-strong -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-freebsd13.2\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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-freebsd13.2\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -fstack-protector-strong -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-freebsd13.2\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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-freebsd13.2\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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] 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 GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #define G_DEPRECATED __attribute__((__deprecated__)) ^ alignment.c:667:9: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] 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 GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #define G_DEPRECATED __attribute__((__deprecated__)) ^ alignment.c:677:13: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] 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 GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #define G_DEPRECATED __attribute__((__deprecated__)) ^ alignment.c:690:9: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] 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 GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #define G_DEPRECATED __attribute__((__deprecated__)) ^ alignment.c:987:5: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] g_strup(qy_codon); ^ /usr/local/include/glib-2.0/glib/gstrfuncs.h:276:1: note: 'g_strup' has been explicitly marked deprecated here GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #define G_DEPRECATED __attribute__((__deprecated__)) ^ alignment.c:988:5: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] g_strup(tg_codon); ^ /usr/local/include/glib-2.0/glib/gstrfuncs.h:276:1: note: 'g_strup' has been explicitly marked deprecated here GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #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 -fstack-protector-strong -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-freebsd13.2\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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-freebsd13.2\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -fstack-protector-strong -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-freebsd13.2\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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-freebsd13.2\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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-freebsd13.2\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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-freebsd13.2\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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] if((macro[i] == '%')){ ~~~~~~~~~^~~~~~ viterbi.c:877:22: note: remove extraneous parentheses around the comparison to silence this warning if((macro[i] == '%')){ ~ ^ ~ viterbi.c:877:22: note: use '=' to turn this equality comparison into an assignment 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-freebsd13.2\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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-freebsd13.2\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -fstack-protector-strong -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-freebsd13.2\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -fstack-protector-strong -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-freebsd13.2\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -fstack-protector-strong -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-freebsd13.2\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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-freebsd13.2\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -fstack-protector-strong -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-freebsd13.2\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -fstack-protector-strong -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-freebsd13.2\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -fstack-protector-strong -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-freebsd13.2\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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-freebsd13.2\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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] 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] 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 -fstack-protector-strong -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-freebsd13.2\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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-freebsd13.2\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -fstack-protector-strong -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-freebsd13.2\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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-freebsd13.2\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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-freebsd13.2\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -fstack-protector-strong -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-freebsd13.2\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -fstack-protector-strong -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-freebsd13.2\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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-freebsd13.2\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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-freebsd13.2\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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-freebsd13.2\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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-freebsd13.2\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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-freebsd13.2\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -fstack-protector-strong -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-freebsd13.2\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -fstack-protector-strong -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-freebsd13.2\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -fstack-protector-strong -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-freebsd13.2\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -fstack-protector-strong -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-freebsd13.2\"" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-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 -fstack-protector-strong -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 -fstack-protector-strong -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 -fstack-protector-strong -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 -fstack-protector-strong -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 -fstack-protector-strong -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 -fstack-protector-strong -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 -fstack-protector-strong -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 -fstack-protector-strong -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 -fstack-protector-strong -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 -fstack-protector-strong -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 -fstack-protector-strong -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 -fstack-protector-strong -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 -fstack-protector-strong -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 -fstack-protector-strong -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 -fstack-protector-strong -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] 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 GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #define G_DEPRECATED __attribute__((__deprecated__)) ^ modeltype.c:124:13: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 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 GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #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 -fstack-protector-strong -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] 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 GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #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 -fstack-protector-strong -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-freebsd13.2\"" -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-freebsd13.2\"" -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] 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 GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #define G_DEPRECATED __attribute__((__deprecated__)) ^ gam.c:526:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] 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 GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #define G_DEPRECATED __attribute__((__deprecated__)) ^ gam.c:539:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] 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 GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #define G_DEPRECATED __attribute__((__deprecated__)) ^ gam.c:589:9: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] 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 GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #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 -fstack-protector-strong -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-freebsd13.2\"" -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-freebsd13.2\"" -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] 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 GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #define G_DEPRECATED __attribute__((__deprecated__)) ^ analysis.c:336:17: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] } 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 GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #define G_DEPRECATED __attribute__((__deprecated__)) ^ analysis.c:337:17: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] || (!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 GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #define G_DEPRECATED __attribute__((__deprecated__)) ^ analysis.c:339:17: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] } 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 GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #define G_DEPRECATED __attribute__((__deprecated__)) ^ analysis.c:340:17: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] || (!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 GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #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-freebsd13.2\"" -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 -fstack-protector-strong -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-freebsd13.2\"" -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 -fstack-protector-strong -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-freebsd13.2\"" -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: 16:07:01.182: Starting building bootstrapping components ** Message: 16:07:01.182: Processing model [u] ** Message: 16:07:01.182: Bootstrapper processing model [ungapped:dna2dna] ** Message: 16:07:01.182: Process optimal [optimal:ungapped:dna2dna] ** (process:47880): WARNING **: 16:07:01.182: Creating codegen directory [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen] ** (process:47880): WARNING **: 16:07:01.182: Creating codegen directory [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen] ** (process:47880): WARNING **: 16:07:01.182: Creating codegen directory [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2] ** (process:47880): WARNING **: 16:07:01.182: Creating codegen directory [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2] ** Message: 16:07:01.183: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_ungapped_58_dna2dna_32_find_32_score.c ** Message: 16:07:01.422: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_ungapped_58_dna2dna_32_find_32_path.c ** Message: 16:07:01.675: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_ungapped_58_dna2dna_32_find_32_region.c ** Message: 16:07:01.949: 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_2/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_2/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.c ** Message: 16:07:02.368: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 16:07:02.722: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_ungapped_58_dna2dna_32_find_32_score.o] ** Message: 16:07:02.722: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_ungapped_58_dna2dna_32_find_32_score.o ** Message: 16:07:02.740: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_score] ** Message: 16:07:02.740: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_ungapped_58_dna2dna_32_find_32_path.o] ** Message: 16:07:02.740: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_ungapped_58_dna2dna_32_find_32_path.o ** Message: 16:07:02.745: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_path] ** Message: 16:07:02.745: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_ungapped_58_dna2dna_32_find_32_region.o] ** Message: 16:07:02.745: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_ungapped_58_dna2dna_32_find_32_region.o ** Message: 16:07:02.750: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_region] ** Message: 16:07:02.750: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.o] ** Message: 16:07:02.751: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.o ** Message: 16:07:02.755: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint] ** Message: 16:07:02.755: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 16:07:02.755: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 16:07:02.759: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation] ** Message: 16:07:02.759: Bootstrapper processing model [ungapped:protein2protein] ** Message: 16:07:02.759: Process optimal [optimal:ungapped:protein2protein] ** Message: 16:07:02.759: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_ungapped_58_protein2protein_32_find_32_score.c ** Message: 16:07:03.108: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_ungapped_58_protein2protein_32_find_32_path.c ** Message: 16:07:03.351: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_ungapped_58_protein2protein_32_find_32_region.c ** Message: 16:07:03.629: 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_2/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_2/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.c ** Message: 16:07:04.068: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.c ** Message: 16:07:04.427: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_ungapped_58_protein2protein_32_find_32_score.o] ** Message: 16:07:04.427: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_ungapped_58_protein2protein_32_find_32_score.o ** Message: 16:07:04.431: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_score] ** Message: 16:07:04.431: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_ungapped_58_protein2protein_32_find_32_path.o] ** Message: 16:07:04.431: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_ungapped_58_protein2protein_32_find_32_path.o ** Message: 16:07:04.436: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_path] ** Message: 16:07:04.436: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_ungapped_58_protein2protein_32_find_32_region.o] ** Message: 16:07:04.436: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_ungapped_58_protein2protein_32_find_32_region.o ** Message: 16:07:04.440: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_region] ** Message: 16:07:04.440: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.o] ** Message: 16:07:04.440: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.o ** Message: 16:07:04.444: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint] ** Message: 16:07:04.444: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.o] ** Message: 16:07:04.444: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.o ** Message: 16:07:04.449: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation] ** Message: 16:07:04.450: Bootstrapper processing model [ungapped:dna2protein] ** Message: 16:07:04.450: Process optimal [optimal:ungapped:dna2protein] ** Message: 16:07:04.450: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_ungapped_58_dna2protein_32_find_32_score.c ** Message: 16:07:04.706: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_ungapped_58_dna2protein_32_find_32_path.c ** Message: 16:07:05.081: 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_2/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_2/optimal_58_ungapped_58_dna2protein_32_find_32_region.c ** Message: 16:07:05.447: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.c ** Message: 16:07:06.068: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.c ** Message: 16:07:06.571: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_ungapped_58_dna2protein_32_find_32_score.o] ** Message: 16:07:06.571: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_ungapped_58_dna2protein_32_find_32_score.o ** Message: 16:07:06.576: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_score] ** Message: 16:07:06.576: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_ungapped_58_dna2protein_32_find_32_path.o] ** Message: 16:07:06.576: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_ungapped_58_dna2protein_32_find_32_path.o ** Message: 16:07:06.581: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_path] ** Message: 16:07:06.581: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_ungapped_58_dna2protein_32_find_32_region.o] ** Message: 16:07:06.581: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_ungapped_58_dna2protein_32_find_32_region.o ** Message: 16:07:06.585: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_region] ** Message: 16:07:06.585: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.o] ** Message: 16:07:06.585: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.o ** Message: 16:07:06.591: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint] ** Message: 16:07:06.591: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.o] ** Message: 16:07:06.591: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.o ** Message: 16:07:06.596: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation] ** Message: 16:07:06.596: Bootstrapper processing model [ungapped:protein2dna] ** Message: 16:07:06.596: Process optimal [optimal:ungapped:protein2dna] ** Message: 16:07:06.596: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_ungapped_58_protein2dna_32_find_32_score.c ** Message: 16:07:06.968: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_ungapped_58_protein2dna_32_find_32_path.c ** Message: 16:07:07.322: 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_2/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_2/optimal_58_ungapped_58_protein2dna_32_find_32_region.c ** Message: 16:07:07.700: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.c ** Message: 16:07:08.265: 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_2/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_2/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.c ** Message: 16:07:08.640: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_ungapped_58_protein2dna_32_find_32_score.o] ** Message: 16:07:08.640: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_ungapped_58_protein2dna_32_find_32_score.o ** Message: 16:07:08.645: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_score] ** Message: 16:07:08.645: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_ungapped_58_protein2dna_32_find_32_path.o] ** Message: 16:07:08.645: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_ungapped_58_protein2dna_32_find_32_path.o ** Message: 16:07:08.649: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_path] ** Message: 16:07:08.649: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_ungapped_58_protein2dna_32_find_32_region.o] ** Message: 16:07:08.649: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_ungapped_58_protein2dna_32_find_32_region.o ** Message: 16:07:08.653: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_region] ** Message: 16:07:08.653: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.o] ** Message: 16:07:08.653: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.o ** Message: 16:07:08.657: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint] ** Message: 16:07:08.658: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.o] ** Message: 16:07:08.658: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.o ** Message: 16:07:08.661: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation] ** Message: 16:07:08.662: Processing model [u:t] ** Message: 16:07:08.662: Bootstrapper processing model [ungapped:codon] ** Message: 16:07:08.662: Process optimal [optimal:ungapped:codon] ** Message: 16:07:08.662: 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_2/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_2/optimal_58_ungapped_58_codon_32_find_32_score.c ** Message: 16:07:09.180: 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_2/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_2/optimal_58_ungapped_58_codon_32_find_32_path.c ** Message: 16:07:09.679: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_ungapped_58_codon_32_find_32_region.c ** Message: 16:07:10.226: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_ungapped_58_codon_32_find_32_checkpoint.c ** Message: 16:07:10.847: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.c ** Message: 16:07:11.311: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_ungapped_58_codon_32_find_32_score.o] ** Message: 16:07:11.311: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_ungapped_58_codon_32_find_32_score.o ** Message: 16:07:11.316: Adding function [optimal_58_ungapped_58_codon_32_find_32_score] ** Message: 16:07:11.316: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_ungapped_58_codon_32_find_32_path.o] ** Message: 16:07:11.316: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_ungapped_58_codon_32_find_32_path.o ** Message: 16:07:11.319: Adding function [optimal_58_ungapped_58_codon_32_find_32_path] ** Message: 16:07:11.319: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_ungapped_58_codon_32_find_32_region.o] ** Message: 16:07:11.319: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_ungapped_58_codon_32_find_32_region.o ** Message: 16:07:11.323: Adding function [optimal_58_ungapped_58_codon_32_find_32_region] ** Message: 16:07:11.323: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_ungapped_58_codon_32_find_32_checkpoint.o] ** Message: 16:07:11.323: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_ungapped_58_codon_32_find_32_checkpoint.o ** Message: 16:07:11.328: Adding function [optimal_58_ungapped_58_codon_32_find_32_checkpoint] ** Message: 16:07:11.328: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.o] ** Message: 16:07:11.328: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.o ** Message: 16:07:11.334: Adding function [optimal_58_ungapped_58_codon_32_find_32_path_32_continuation] ** Message: 16:07:11.334: Processing model [a:g] ** Message: 16:07:11.334: Bootstrapper processing model [affine:global:dna2dna] ** Message: 16:07:11.334: Process optimal [optimal:affine:global:dna2dna] ** Message: 16:07:11.335: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.c ** Message: 16:07:11.870: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.c ** Message: 16:07:12.351: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.c ** Message: 16:07:13.009: 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_2/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_2/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 16:07:13.689: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.o] ** Message: 16:07:13.689: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.o ** Message: 16:07:13.695: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_score] ** Message: 16:07:13.695: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.o] ** Message: 16:07:13.695: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.o ** Message: 16:07:13.701: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_path] ** Message: 16:07:13.701: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.o] ** Message: 16:07:13.701: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.o ** Message: 16:07:13.706: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint] ** Message: 16:07:13.706: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 16:07:13.706: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 16:07:13.711: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation] ** Message: 16:07:13.712: Bootstrapper processing model [affine:global:protein2protein] ** Message: 16:07:13.712: Process optimal [optimal:affine:global:protein2protein] ** Message: 16:07:13.713: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.c ** Message: 16:07:14.551: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.c ** Message: 16:07:15.168: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.c ** Message: 16:07:15.790: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.c ** Message: 16:07:16.285: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.o] ** Message: 16:07:16.285: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.o ** Message: 16:07:16.291: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_score] ** Message: 16:07:16.291: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.o] ** Message: 16:07:16.291: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.o ** Message: 16:07:16.296: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_path] ** Message: 16:07:16.296: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.o] ** Message: 16:07:16.296: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.o ** Message: 16:07:16.302: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint] ** Message: 16:07:16.302: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.o] ** Message: 16:07:16.302: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.o ** Message: 16:07:16.308: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation] ** Message: 16:07:16.308: Processing model [a:b] ** Message: 16:07:16.308: Bootstrapper processing model [affine:bestfit:dna2dna] ** Message: 16:07:16.308: Process optimal [optimal:affine:bestfit:dna2dna] ** Message: 16:07:16.310: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.c ** Message: 16:07:16.957: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.c ** Message: 16:07:17.751: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.c ** Message: 16:07:18.425: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.c ** Message: 16:07:19.030: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 16:07:19.597: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.o] ** Message: 16:07:19.597: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.o ** Message: 16:07:19.603: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score] ** Message: 16:07:19.603: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.o] ** Message: 16:07:19.603: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.o ** Message: 16:07:19.609: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path] ** Message: 16:07:19.609: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.o] ** Message: 16:07:19.609: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.o ** Message: 16:07:19.614: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region] ** Message: 16:07:19.614: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.o] ** Message: 16:07:19.614: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.o ** Message: 16:07:19.620: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint] ** Message: 16:07:19.620: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 16:07:19.620: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 16:07:19.624: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation] ** Message: 16:07:19.624: Bootstrapper processing model [affine:bestfit:protein2protein] ** Message: 16:07:19.624: Process optimal [optimal:affine:bestfit:protein2protein] ** Message: 16:07:19.625: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.c ** Message: 16:07:20.292: 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_2/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_2/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.c ** Message: 16:07:21.007: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.c ** Message: 16:07:21.896: 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_2/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_2/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.c ** Message: 16:07:22.610: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.c ** Message: 16:07:23.164: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.o] ** Message: 16:07:23.164: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.o ** Message: 16:07:23.168: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score] ** Message: 16:07:23.168: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.o] ** Message: 16:07:23.168: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.o ** Message: 16:07:23.172: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path] ** Message: 16:07:23.172: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.o] ** Message: 16:07:23.172: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.o ** Message: 16:07:23.176: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region] ** Message: 16:07:23.176: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.o] ** Message: 16:07:23.176: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.o ** Message: 16:07:23.180: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint] ** Message: 16:07:23.180: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.o] ** Message: 16:07:23.180: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.o ** Message: 16:07:23.184: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation] ** Message: 16:07:23.184: Processing model [a:l] ** Message: 16:07:23.184: Bootstrapper processing model [affine:local:dna2dna] ** Message: 16:07:23.184: Process optimal [optimal:affine:local:dna2dna] ** Message: 16:07:23.184: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.c ** Message: 16:07:23.437: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.c ** Message: 16:07:23.730: 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_2/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_2/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.c ** Message: 16:07:24.074: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.c ** Message: 16:07:24.818: 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_2/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_2/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 16:07:25.278: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.o] ** Message: 16:07:25.278: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.o ** Message: 16:07:25.283: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_score] ** Message: 16:07:25.283: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.o] ** Message: 16:07:25.283: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.o ** Message: 16:07:25.287: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_path] ** Message: 16:07:25.287: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.o] ** Message: 16:07:25.287: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.o ** Message: 16:07:25.291: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_region] ** Message: 16:07:25.291: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o] ** Message: 16:07:25.291: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o ** Message: 16:07:25.295: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint] ** Message: 16:07:25.295: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 16:07:25.295: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 16:07:25.298: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation] ** Message: 16:07:25.301: Process optimal [Terminal [Segment("START"->"match"):[affine:local:dna2dna]]] ** Message: 16:07:25.302: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.c ** Message: 16:07:26.101: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.c ** Message: 16:07:26.662: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] ** Message: 16:07:26.662: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o ** Message: 16:07:26.667: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score] ** Message: 16:07:26.667: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 16:07:26.667: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 16:07:26.671: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path] ** Message: 16:07:26.671: Process optimal [Terminal [Segment("match"->"END"):[affine:local:dna2dna]]] ** Message: 16:07:26.672: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.c ** Message: 16:07:27.374: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.c ** Message: 16:07:28.080: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] ** Message: 16:07:28.080: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o ** Message: 16:07:28.086: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score] ** Message: 16:07:28.087: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 16:07:28.087: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 16:07:28.093: 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: 16:07:28.093: Process optimal [HeuristicJoin:[Segment("match"->"match"):[affine:local:dna2dna]]] ** Message: 16:07:28.095: 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_2/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_2/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.c ** Message: 16:07:29.115: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.c ** Message: 16:07:30.513: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] ** Message: 16:07:30.513: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o ** Message: 16:07:30.520: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score] ** Message: 16:07:30.520: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 16:07:30.520: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 16:07:30.525: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path] ** Message: 16:07:30.525: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.c ** Message: 16:07:30.859: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.c ** Message: 16:07:31.197: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.o] ** Message: 16:07:31.197: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.o ** Message: 16:07:31.204: Adding function [Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded] ** Message: 16:07:31.204: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.o] ** Message: 16:07:31.204: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.o ** Message: 16:07:31.210: Adding function [Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded] ** Message: 16:07:31.211: Bootstrapper processing model [affine:local:protein2protein] ** Message: 16:07:31.211: Process optimal [optimal:affine:local:protein2protein] ** Message: 16:07:31.211: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.c ** Message: 16:07:31.632: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.c ** Message: 16:07:32.036: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.c ** Message: 16:07:32.329: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.c ** Message: 16:07:33.215: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.c ** Message: 16:07:33.664: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.o] ** Message: 16:07:33.664: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.o ** Message: 16:07:33.671: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_score] ** Message: 16:07:33.671: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.o] ** Message: 16:07:33.671: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.o ** Message: 16:07:33.676: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_path] ** Message: 16:07:33.676: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.o] ** Message: 16:07:33.676: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.o ** Message: 16:07:33.680: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_region] ** Message: 16:07:33.680: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o] ** Message: 16:07:33.680: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o ** Message: 16:07:33.684: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint] ** Message: 16:07:33.685: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o] ** Message: 16:07:33.685: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o ** Message: 16:07:33.689: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation] ** Message: 16:07:33.690: Process optimal [Terminal [Segment("START"->"match"):[affine:local:protein2protein]]] ** Message: 16:07:33.691: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.c ** Message: 16:07:34.111: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.c ** Message: 16:07:34.816: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] ** Message: 16:07:34.816: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o ** Message: 16:07:34.823: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score] ** Message: 16:07:34.824: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 16:07:34.824: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 16:07:34.829: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path] ** Message: 16:07:34.829: Process optimal [Terminal [Segment("match"->"END"):[affine:local:protein2protein]]] ** Message: 16:07:34.829: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.c ** Message: 16:07:35.176: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.c ** Message: 16:07:35.800: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] ** Message: 16:07:35.800: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o ** Message: 16:07:35.807: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score] ** Message: 16:07:35.807: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 16:07:35.807: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 16:07:35.814: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path] ** Message: 16:07:35.814: Process optimal [HeuristicJoin:[Segment("match"->"match"):[affine:local:protein2protein]]] ** Message: 16:07:35.815: 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_2/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_2/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.c ** Message: 16:07:36.820: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.c ** Message: 16:07:37.805: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] ** Message: 16:07:37.805: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o ** Message: 16:07:37.812: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score] ** Message: 16:07:37.812: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 16:07:37.812: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 16:07:37.817: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path] ** Message: 16:07:37.817: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.c ** Message: 16:07:38.116: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.c ** Message: 16:07:38.480: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.o] ** Message: 16:07:38.480: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.o ** Message: 16:07:38.487: Adding function [Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded] ** Message: 16:07:38.487: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.o] ** Message: 16:07:38.487: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.o ** Message: 16:07:38.491: Adding function [Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded] ** Message: 16:07:38.491: Processing model [a:o] ** Message: 16:07:38.492: Bootstrapper processing model [affine:overlap:dna2dna] ** Message: 16:07:38.492: Process optimal [optimal:affine:overlap:dna2dna] ** Message: 16:07:38.492: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.c ** Message: 16:07:38.985: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.c ** Message: 16:07:39.519: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.c ** Message: 16:07:40.074: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.c ** Message: 16:07:40.751: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 16:07:41.289: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.o] ** Message: 16:07:41.289: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.o ** Message: 16:07:41.296: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score] ** Message: 16:07:41.296: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.o] ** Message: 16:07:41.296: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.o ** Message: 16:07:41.303: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path] ** Message: 16:07:41.303: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.o] ** Message: 16:07:41.303: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.o ** Message: 16:07:41.309: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region] ** Message: 16:07:41.309: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.o] ** Message: 16:07:41.309: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.o ** Message: 16:07:41.314: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint] ** Message: 16:07:41.314: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 16:07:41.314: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 16:07:41.318: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation] ** Message: 16:07:41.318: Processing model [e2g] ** Message: 16:07:41.318: Bootstrapper processing model [est2genome] ** Message: 16:07:41.318: Process optimal [optimal:est2genome] ** Message: 16:07:41.319: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_est2genome_32_find_32_score.c ** Message: 16:07:42.028: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_est2genome_32_find_32_path.c ** Message: 16:07:42.692: 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_2/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_2/optimal_58_est2genome_32_find_32_region.c ** Message: 16:07:43.516: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_est2genome_32_find_32_checkpoint.c ** Message: 16:07:45.260: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_est2genome_32_find_32_path_32_continuation.c ** Message: 16:07:47.363: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_est2genome_32_find_32_score.o] ** Message: 16:07:47.363: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_est2genome_32_find_32_score.o ** Message: 16:07:47.370: Adding function [optimal_58_est2genome_32_find_32_score] ** Message: 16:07:47.370: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_est2genome_32_find_32_path.o] ** Message: 16:07:47.370: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_est2genome_32_find_32_path.o ** Message: 16:07:47.377: Adding function [optimal_58_est2genome_32_find_32_path] ** Message: 16:07:47.377: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_est2genome_32_find_32_region.o] ** Message: 16:07:47.377: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_est2genome_32_find_32_region.o ** Message: 16:07:47.383: Adding function [optimal_58_est2genome_32_find_32_region] ** Message: 16:07:47.383: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_est2genome_32_find_32_checkpoint.o] ** Message: 16:07:47.383: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_est2genome_32_find_32_checkpoint.o ** Message: 16:07:47.389: Adding function [optimal_58_est2genome_32_find_32_checkpoint] ** Message: 16:07:47.389: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_est2genome_32_find_32_path_32_continuation.o] ** Message: 16:07:47.389: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_est2genome_32_find_32_path_32_continuation.o ** Message: 16:07:47.394: Adding function [optimal_58_est2genome_32_find_32_path_32_continuation] ** Message: 16:07:47.402: Process optimal [Terminal [Segment("START"->"match reverse"):[est2genome]]] ** Message: 16:07:47.404: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 16:07:48.178: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 16:07:49.048: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 16:07:49.048: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 16:07:49.054: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score] ** Message: 16:07:49.054: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 16:07:49.054: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 16:07:49.061: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 16:07:49.061: Process optimal [Terminal [Segment("match reverse"->"END"):[est2genome]]] ** Message: 16:07:49.063: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 16:07:49.619: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 16:07:50.421: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 16:07:50.421: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 16:07:50.426: Adding function [Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score] ** Message: 16:07:50.426: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 16:07:50.426: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 16:07:50.431: Adding function [Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 16:07:50.431: Process optimal [Terminal [Segment("START"->"match forward"):[est2genome]]] ** Message: 16:07:50.432: 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_2/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_2/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 16:07:51.183: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 16:07:52.272: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 16:07:52.272: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 16:07:52.279: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score] ** Message: 16:07:52.279: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 16:07:52.279: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 16:07:52.287: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 16:07:52.287: Process optimal [Terminal [Segment("match forward"->"END"):[est2genome]]] ** Message: 16:07:52.287: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 16:07:52.824: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 16:07:53.433: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 16:07:53.433: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 16:07:53.441: Adding function [Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score] ** Message: 16:07:53.441: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 16:07:53.441: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 16:07:53.449: Adding function [Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 16:07:53.449: Process optimal [HeuristicJoin:[Segment("match reverse"->"match reverse"):[est2genome]]] ** Message: 16:07:53.453: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 16:07:54.945: 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_2/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_2/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 16:07:57.037: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 16:07:57.037: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 16:07:57.043: Adding function [HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score] ** Message: 16:07:57.043: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 16:07:57.043: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 16:07:57.049: Adding function [HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 16:07:57.049: Process optimal [Src span [Segment("match reverse"->"intron reverse"):[est2genome]]] ** Message: 16:07:57.051: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 16:07:57.798: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 16:07:58.464: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 16:07:58.464: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 16:07:58.471: Adding function [Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score] ** Message: 16:07:58.471: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 16:07:58.471: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 16:07:58.477: Adding function [Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 16:07:58.477: Process optimal [Src span traceback [Segment("match reverse"->"intron reverse"):[est2genome]]] ** Message: 16:07:58.479: 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_2/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_2/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 16:08:00.011: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 16:08:00.011: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 16:08:00.019: Adding function [Src_32_span_32_traceback_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 16:08:00.019: Process optimal [Dst span [Segment("intron reverse"->"match reverse"):[est2genome]]] ** Message: 16:08:00.022: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 16:08:00.854: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 16:08:01.884: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 16:08:01.884: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 16:08:01.890: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score] ** Message: 16:08:01.890: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 16:08:01.890: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 16:08:01.895: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 16:08:01.895: Process optimal [HeuristicJoin:[Segment("match forward"->"match forward"):[est2genome]]] ** Message: 16:08:01.900: 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_2/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_2/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 16:08:03.575: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 16:08:04.947: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 16:08:04.947: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 16:08:04.956: Adding function [HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score] ** Message: 16:08:04.956: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 16:08:04.956: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 16:08:04.963: Adding function [HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 16:08:04.963: Process optimal [Src span [Segment("match forward"->"intron forward"):[est2genome]]] ** Message: 16:08:04.964: 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_2/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_2/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 16:08:05.534: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 16:08:06.297: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 16:08:06.297: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 16:08:06.305: Adding function [Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score] ** Message: 16:08:06.305: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 16:08:06.305: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 16:08:06.314: Adding function [Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 16:08:06.314: Process optimal [Src span traceback [Segment("match forward"->"intron forward"):[est2genome]]] ** Message: 16:08:06.317: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 16:08:08.084: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 16:08:08.084: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 16:08:08.092: Adding function [Src_32_span_32_traceback_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 16:08:08.093: Process optimal [Dst span [Segment("intron forward"->"match forward"):[est2genome]]] ** Message: 16:08:08.095: 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_2/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_2/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 16:08:09.323: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 16:08:10.169: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 16:08:10.169: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 16:08:10.175: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score] ** Message: 16:08:10.175: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 16:08:10.175: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 16:08:10.183: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 16:08:10.184: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.c ** Message: 16:08:10.736: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.c ** Message: 16:08:11.350: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.o] ** Message: 16:08:11.350: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.o ** Message: 16:08:11.359: Adding function [Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary] ** Message: 16:08:11.359: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.o] ** Message: 16:08:11.359: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.o ** Message: 16:08:11.368: Adding function [Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary] ** Message: 16:08:11.368: Processing model [ner] ** Message: 16:08:11.369: Bootstrapper processing model [NER:affine:local:dna2dna] ** Message: 16:08:11.369: Process optimal [optimal:NER:affine:local:dna2dna] ** Message: 16:08:11.369: 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_2/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_2/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.c ** Message: 16:08:11.781: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.c ** Message: 16:08:12.260: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.c ** Message: 16:08:12.643: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.c ** Message: 16:08:13.168: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.c ** Message: 16:08:14.025: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.o] ** Message: 16:08:14.025: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.o ** Message: 16:08:14.034: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score] ** Message: 16:08:14.034: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.o] ** Message: 16:08:14.034: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.o ** Message: 16:08:14.042: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path] ** Message: 16:08:14.042: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.o] ** Message: 16:08:14.042: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.o ** Message: 16:08:14.051: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region] ** Message: 16:08:14.051: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o] ** Message: 16:08:14.051: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o ** Message: 16:08:14.059: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint] ** Message: 16:08:14.059: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o] ** Message: 16:08:14.060: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o ** Message: 16:08:14.068: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation] ** Message: 16:08:14.072: Process optimal [Terminal [Segment("START"->"match"):[NER:affine:local:dna2dna]]] ** Message: 16:08:14.073: 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_2/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_2/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.c ** Message: 16:08:14.780: 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_2/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_2/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.c ** Message: 16:08:15.632: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] ** Message: 16:08:15.632: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o ** Message: 16:08:15.641: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score] ** Message: 16:08:15.641: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 16:08:15.641: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 16:08:15.650: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path] ** Message: 16:08:15.650: Process optimal [Terminal [Segment("match"->"END"):[NER:affine:local:dna2dna]]] ** Message: 16:08:15.651: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.c ** Message: 16:08:16.019: 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_2/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_2/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.c ** Message: 16:08:16.927: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] ** Message: 16:08:16.927: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o ** Message: 16:08:16.936: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score] ** Message: 16:08:16.936: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 16:08:16.936: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 16:08:16.945: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path] ** Message: 16:08:16.945: Process optimal [HeuristicJoin:[Segment("match"->"match"):[NER:affine:local:dna2dna]]] ** Message: 16:08:16.948: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.c ** Message: 16:08:17.948: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.c ** Message: 16:08:19.374: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] ** Message: 16:08:19.374: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o ** Message: 16:08:19.382: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score] ** Message: 16:08:19.382: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 16:08:19.382: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 16:08:19.391: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path] ** Message: 16:08:19.391: Process optimal [Src span [Segment("match"->"ner"):[NER:affine:local:dna2dna]]] ** Message: 16:08:19.392: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.c ** Message: 16:08:19.819: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.c ** Message: 16:08:20.422: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] ** Message: 16:08:20.422: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o ** Message: 16:08:20.431: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score] ** Message: 16:08:20.431: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 16:08:20.431: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 16:08:20.438: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path] ** Message: 16:08:20.438: Process optimal [Src span traceback [Segment("match"->"ner"):[NER:affine:local:dna2dna]]] ** Message: 16:08:20.439: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.c ** Message: 16:08:21.705: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 16:08:21.705: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 16:08:21.713: Adding function [Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path] ** Message: 16:08:21.714: Process optimal [Dst span [Segment("ner"->"match"):[NER:affine:local:dna2dna]]] ** Message: 16:08:21.715: 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_2/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_2/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.c ** Message: 16:08:22.530: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.c ** Message: 16:08:23.687: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] ** Message: 16:08:23.687: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o ** Message: 16:08:23.695: Adding function [Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score] ** Message: 16:08:23.696: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] ** Message: 16:08:23.696: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o ** Message: 16:08:23.705: Adding function [Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path] ** Message: 16:08:23.706: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.c ** Message: 16:08:24.141: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.c ** Message: 16:08:24.666: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.o] ** Message: 16:08:24.666: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.o ** Message: 16:08:24.673: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary] ** Message: 16:08:24.673: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.o] ** Message: 16:08:24.673: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.o ** Message: 16:08:24.680: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary] ** Message: 16:08:24.681: Bootstrapper processing model [NER:affine:local:protein2protein] ** Message: 16:08:24.681: Process optimal [optimal:NER:affine:local:protein2protein] ** Message: 16:08:24.681: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.c ** Message: 16:08:25.003: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.c ** Message: 16:08:25.303: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.c ** Message: 16:08:25.635: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.c ** Message: 16:08:26.162: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.c ** Message: 16:08:26.834: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.o] ** Message: 16:08:26.834: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.o ** Message: 16:08:26.844: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score] ** Message: 16:08:26.844: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.o] ** Message: 16:08:26.844: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.o ** Message: 16:08:26.852: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path] ** Message: 16:08:26.852: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.o] ** Message: 16:08:26.852: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.o ** Message: 16:08:26.859: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region] ** Message: 16:08:26.859: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o] ** Message: 16:08:26.859: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o ** Message: 16:08:26.865: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint] ** Message: 16:08:26.865: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o] ** Message: 16:08:26.865: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o ** Message: 16:08:26.871: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation] ** Message: 16:08:26.875: Process optimal [Terminal [Segment("START"->"match"):[NER:affine:local:protein2protein]]] ** Message: 16:08:26.876: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.c ** Message: 16:08:27.527: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.c ** Message: 16:08:28.401: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] ** Message: 16:08:28.401: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o ** Message: 16:08:28.410: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score] ** Message: 16:08:28.411: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 16:08:28.411: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 16:08:28.417: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path] ** Message: 16:08:28.417: Process optimal [Terminal [Segment("match"->"END"):[NER:affine:local:protein2protein]]] ** Message: 16:08:28.418: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.c ** Message: 16:08:28.922: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.c ** Message: 16:08:29.413: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] ** Message: 16:08:29.413: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o ** Message: 16:08:29.422: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score] ** Message: 16:08:29.422: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 16:08:29.422: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 16:08:29.432: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path] ** Message: 16:08:29.432: Process optimal [HeuristicJoin:[Segment("match"->"match"):[NER:affine:local:protein2protein]]] ** Message: 16:08:29.435: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.c ** Message: 16:08:30.531: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.c ** Message: 16:08:31.922: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] ** Message: 16:08:31.922: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o ** Message: 16:08:31.932: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score] ** Message: 16:08:31.932: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 16:08:31.933: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 16:08:31.943: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path] ** Message: 16:08:31.943: Process optimal [Src span [Segment("match"->"ner"):[NER:affine:local:protein2protein]]] ** Message: 16:08:31.944: 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_2/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_2/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.c ** Message: 16:08:32.559: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.c ** Message: 16:08:33.130: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] ** Message: 16:08:33.130: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o ** Message: 16:08:33.141: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score] ** Message: 16:08:33.141: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 16:08:33.141: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 16:08:33.150: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path] ** Message: 16:08:33.150: Process optimal [Src span traceback [Segment("match"->"ner"):[NER:affine:local:protein2protein]]] ** Message: 16:08:33.153: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.c ** Message: 16:08:34.015: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 16:08:34.015: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 16:08:34.024: Adding function [Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path] ** Message: 16:08:34.024: Process optimal [Dst span [Segment("ner"->"match"):[NER:affine:local:protein2protein]]] ** Message: 16:08:34.026: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.c ** Message: 16:08:34.562: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.c ** Message: 16:08:35.275: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] ** Message: 16:08:35.275: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o ** Message: 16:08:35.285: Adding function [Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score] ** Message: 16:08:35.285: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] ** Message: 16:08:35.285: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o ** Message: 16:08:35.295: Adding function [Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path] ** Message: 16:08:35.296: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.c ** Message: 16:08:35.663: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.c ** Message: 16:08:35.990: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.o] ** Message: 16:08:35.990: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.o ** Message: 16:08:35.998: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary] ** Message: 16:08:35.998: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.o] ** Message: 16:08:35.998: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.o ** Message: 16:08:36.006: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary] ** Message: 16:08:36.006: Processing model [p2d] ** Message: 16:08:36.006: Bootstrapper processing model [protein2dna:local] ** Message: 16:08:36.006: Process optimal [optimal:protein2dna:local] ** Message: 16:08:36.007: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_protein2dna_58_local_32_find_32_score.c ** Message: 16:08:36.475: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_protein2dna_58_local_32_find_32_path.c ** Message: 16:08:36.900: 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_2/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_2/optimal_58_protein2dna_58_local_32_find_32_region.c ** Message: 16:08:37.653: 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_2/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_2/optimal_58_protein2dna_58_local_32_find_32_checkpoint.c ** Message: 16:08:38.763: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.c ** Message: 16:08:39.569: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_protein2dna_58_local_32_find_32_score.o] ** Message: 16:08:39.569: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_protein2dna_58_local_32_find_32_score.o ** Message: 16:08:39.580: Adding function [optimal_58_protein2dna_58_local_32_find_32_score] ** Message: 16:08:39.580: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_protein2dna_58_local_32_find_32_path.o] ** Message: 16:08:39.580: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_protein2dna_58_local_32_find_32_path.o ** Message: 16:08:39.590: Adding function [optimal_58_protein2dna_58_local_32_find_32_path] ** Message: 16:08:39.590: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_protein2dna_58_local_32_find_32_region.o] ** Message: 16:08:39.590: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_protein2dna_58_local_32_find_32_region.o ** Message: 16:08:39.600: Adding function [optimal_58_protein2dna_58_local_32_find_32_region] ** Message: 16:08:39.600: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_protein2dna_58_local_32_find_32_checkpoint.o] ** Message: 16:08:39.600: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_protein2dna_58_local_32_find_32_checkpoint.o ** Message: 16:08:39.611: Adding function [optimal_58_protein2dna_58_local_32_find_32_checkpoint] ** Message: 16:08:39.611: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.o] ** Message: 16:08:39.611: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.o ** Message: 16:08:39.621: Adding function [optimal_58_protein2dna_58_local_32_find_32_path_32_continuation] ** Message: 16:08:39.629: Process optimal [Terminal [Segment("START"->"match"):[protein2dna:local]]] ** Message: 16:08:39.632: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.c ** Message: 16:08:40.445: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.c ** Message: 16:08:41.544: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] ** Message: 16:08:41.544: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o ** Message: 16:08:41.555: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score] ** Message: 16:08:41.555: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] ** Message: 16:08:41.555: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o ** Message: 16:08:41.566: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path] ** Message: 16:08:41.566: Process optimal [Terminal [Segment("match"->"END"):[protein2dna:local]]] ** Message: 16:08:41.567: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.c ** Message: 16:08:42.209: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.c ** Message: 16:08:42.849: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] ** Message: 16:08:42.849: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o ** Message: 16:08:42.859: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score] ** Message: 16:08:42.859: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] ** Message: 16:08:42.859: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o ** Message: 16:08:42.870: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path] ** Message: 16:08:42.870: Process optimal [HeuristicJoin:[Segment("match"->"match"):[protein2dna:local]]] ** Message: 16:08:42.873: 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_2/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_2/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.c ** Message: 16:08:44.040: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.c ** Message: 16:08:45.875: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] ** Message: 16:08:45.875: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o ** Message: 16:08:45.883: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score] ** Message: 16:08:45.883: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] ** Message: 16:08:45.883: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o ** Message: 16:08:45.890: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path] ** Message: 16:08:45.891: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.c ** Message: 16:08:46.257: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.c ** Message: 16:08:46.581: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.o] ** Message: 16:08:46.581: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.o ** Message: 16:08:46.591: Adding function [Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded] ** Message: 16:08:46.591: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.o] ** Message: 16:08:46.591: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.o ** Message: 16:08:46.601: Adding function [Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded] ** Message: 16:08:46.601: Processing model [p2d:b] ** Message: 16:08:46.601: Bootstrapper processing model [protein2dna:bestfit] ** Message: 16:08:46.601: Process optimal [optimal:protein2dna:bestfit] ** Message: 16:08:46.604: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_protein2dna_58_bestfit_32_find_32_score.c ** Message: 16:08:47.779: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_protein2dna_58_bestfit_32_find_32_path.c ** Message: 16:08:49.264: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_protein2dna_58_bestfit_32_find_32_region.c ** Message: 16:08:50.626: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.c ** Message: 16:08:51.462: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.c ** Message: 16:08:52.291: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_protein2dna_58_bestfit_32_find_32_score.o] ** Message: 16:08:52.291: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_protein2dna_58_bestfit_32_find_32_score.o ** Message: 16:08:52.299: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_score] ** Message: 16:08:52.299: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_protein2dna_58_bestfit_32_find_32_path.o] ** Message: 16:08:52.299: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_protein2dna_58_bestfit_32_find_32_path.o ** Message: 16:08:52.307: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_path] ** Message: 16:08:52.307: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_protein2dna_58_bestfit_32_find_32_region.o] ** Message: 16:08:52.307: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_protein2dna_58_bestfit_32_find_32_region.o ** Message: 16:08:52.314: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_region] ** Message: 16:08:52.315: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.o] ** Message: 16:08:52.315: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.o ** Message: 16:08:52.322: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint] ** Message: 16:08:52.322: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.o] ** Message: 16:08:52.322: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.o ** Message: 16:08:52.329: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation] ** Message: 16:08:52.330: Processing model [p2g] ** Message: 16:08:52.330: Bootstrapper processing model [protein2genome:local] ** Message: 16:08:52.330: Process optimal [optimal:protein2genome:local] ** Message: 16:08:52.331: 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_2/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_2/optimal_58_protein2genome_58_local_32_find_32_score.c ** Message: 16:08:53.192: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_protein2genome_58_local_32_find_32_path.c ** Message: 16:08:53.950: 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_2/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_2/optimal_58_protein2genome_58_local_32_find_32_region.c ** Message: 16:08:54.902: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_protein2genome_58_local_32_find_32_checkpoint.c ** Message: 16:08:57.014: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.c ** Message: 16:08:59.016: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_protein2genome_58_local_32_find_32_score.o] ** Message: 16:08:59.016: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_protein2genome_58_local_32_find_32_score.o ** Message: 16:08:59.025: Adding function [optimal_58_protein2genome_58_local_32_find_32_score] ** Message: 16:08:59.025: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_protein2genome_58_local_32_find_32_path.o] ** Message: 16:08:59.025: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_protein2genome_58_local_32_find_32_path.o ** Message: 16:08:59.033: Adding function [optimal_58_protein2genome_58_local_32_find_32_path] ** Message: 16:08:59.033: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_protein2genome_58_local_32_find_32_region.o] ** Message: 16:08:59.033: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_protein2genome_58_local_32_find_32_region.o ** Message: 16:08:59.042: Adding function [optimal_58_protein2genome_58_local_32_find_32_region] ** Message: 16:08:59.042: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_protein2genome_58_local_32_find_32_checkpoint.o] ** Message: 16:08:59.042: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_protein2genome_58_local_32_find_32_checkpoint.o ** Message: 16:08:59.051: Adding function [optimal_58_protein2genome_58_local_32_find_32_checkpoint] ** Message: 16:08:59.051: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.o] ** Message: 16:08:59.051: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.o ** Message: 16:08:59.061: Adding function [optimal_58_protein2genome_58_local_32_find_32_path_32_continuation] ** Message: 16:08:59.093: Process optimal [Terminal [Segment("START"->"match"):[protein2genome:local]]] ** Message: 16:08:59.098: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 16:09:01.470: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 16:09:04.049: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 16:09:04.049: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 16:09:04.060: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score] ** Message: 16:09:04.060: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 16:09:04.060: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 16:09:04.073: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] ** Message: 16:09:04.073: Process optimal [Terminal [Segment("match"->"END"):[protein2genome:local]]] ** Message: 16:09:04.076: 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_2/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_2/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 16:09:05.237: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 16:09:06.885: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 16:09:06.885: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 16:09:06.897: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score] ** Message: 16:09:06.897: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 16:09:06.897: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 16:09:06.908: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] ** Message: 16:09:06.908: Process optimal [HeuristicJoin:[Segment("match"->"match"):[protein2genome:local]]] ** Message: 16:09:06.914: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 16:09:10.314: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/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: 16:09:14.815: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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: 16:09:14.816: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/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: 16:09:14.824: 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: 16:09:14.825: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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: 16:09:14.825: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/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: 16:09:14.833: 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: 16:09:14.833: Process optimal [Src span [Segment("match"->"intron 0:0 phase-T"):[protein2genome:local]]] ** Message: 16:09:14.835: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/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: 16:09:15.954: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/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: 16:09:17.456: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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: 16:09:17.456: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/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: 16:09:17.466: 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: 16:09:17.466: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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: 16:09:17.466: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/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: 16:09:17.474: 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: 16:09:17.474: Process optimal [Src span traceback [Segment("match"->"intron 0:0 phase-T"):[protein2genome:local]]] ** Message: 16:09:17.484: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/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: 16:09:21.883: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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: 16:09:21.883: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/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: 16:09:21.891: 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: 16:09:21.891: Process optimal [Dst span [Segment("intron 0:0 phase-T"->"match"):[protein2genome:local]]] ** Message: 16:09:21.894: 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_2/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_2/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: 16:09:23.951: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/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: 16:09:26.947: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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: 16:09:26.947: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/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: 16:09:26.957: 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: 16:09:26.957: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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: 16:09:26.957: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/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: 16:09:26.970: 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: 16:09:26.970: Process optimal [Src span [Segment("match"->"intron 1:2 phase-T"):[protein2genome:local]]] ** Message: 16:09:26.972: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/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: 16:09:27.972: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/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: 16:09:29.317: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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: 16:09:29.317: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/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: 16:09:29.328: 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: 16:09:29.328: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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: 16:09:29.328: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/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: 16:09:29.342: 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: 16:09:29.342: Process optimal [Src span traceback [Segment("match"->"intron 1:2 phase-T"):[protein2genome:local]]] ** Message: 16:09:29.351: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/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: 16:09:33.616: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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: 16:09:33.616: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/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: 16:09:33.629: 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: 16:09:33.629: Process optimal [Dst span [Segment("intron 1:2 phase-T"->"match"):[protein2genome:local]]] ** Message: 16:09:33.634: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/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: 16:09:35.263: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/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: 16:09:38.464: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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: 16:09:38.464: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/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: 16:09:38.478: 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: 16:09:38.478: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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: 16:09:38.478: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/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: 16:09:38.491: 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: 16:09:38.491: Process optimal [Src span [Segment("match"->"intron 2:1 phase-T"):[protein2genome:local]]] ** Message: 16:09:38.493: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/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: 16:09:39.556: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/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: 16:09:41.078: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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: 16:09:41.078: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/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: 16:09:41.091: 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: 16:09:41.091: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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: 16:09:41.091: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/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: 16:09:41.103: 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: 16:09:41.103: Process optimal [Src span traceback [Segment("match"->"intron 2:1 phase-T"):[protein2genome:local]]] ** Message: 16:09:41.113: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/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: 16:09:46.094: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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: 16:09:46.094: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/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: 16:09:46.106: 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: 16:09:46.106: Process optimal [Dst span [Segment("intron 2:1 phase-T"->"match"):[protein2genome:local]]] ** Message: 16:09:46.112: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/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: 16:09:48.242: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/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: 16:09:50.807: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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: 16:09:50.807: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/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: 16:09:50.817: 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: 16:09:50.817: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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: 16:09:50.817: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/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: 16:09:50.826: 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: 16:09:50.827: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.c ** Message: 16:09:51.144: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.c ** Message: 16:09:51.765: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.o] ** Message: 16:09:51.765: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.o ** Message: 16:09:51.780: Adding function [Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary] ** Message: 16:09:51.780: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.o] ** Message: 16:09:51.780: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.o ** Message: 16:09:51.793: Adding function [Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary] ** Message: 16:09:51.794: Processing model [p2g:b] ** Message: 16:09:51.794: Bootstrapper processing model [protein2genome:bestfit] ** Message: 16:09:51.795: Process optimal [optimal:protein2genome:bestfit] ** Message: 16:09:51.801: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_protein2genome_58_bestfit_32_find_32_score.c ** Message: 16:09:54.676: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_protein2genome_58_bestfit_32_find_32_path.c ** Message: 16:09:57.584: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_protein2genome_58_bestfit_32_find_32_region.c ** Message: 16:10:00.720: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.c ** Message: 16:10:02.702: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.c ** Message: 16:10:05.458: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_protein2genome_58_bestfit_32_find_32_score.o] ** Message: 16:10:05.458: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_protein2genome_58_bestfit_32_find_32_score.o ** Message: 16:10:05.469: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_score] ** Message: 16:10:05.470: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_protein2genome_58_bestfit_32_find_32_path.o] ** Message: 16:10:05.470: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_protein2genome_58_bestfit_32_find_32_path.o ** Message: 16:10:05.484: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_path] ** Message: 16:10:05.484: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_protein2genome_58_bestfit_32_find_32_region.o] ** Message: 16:10:05.484: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_protein2genome_58_bestfit_32_find_32_region.o ** Message: 16:10:05.499: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_region] ** Message: 16:10:05.499: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.o] ** Message: 16:10:05.499: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.o ** Message: 16:10:05.512: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint] ** Message: 16:10:05.512: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.o] ** Message: 16:10:05.512: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.o ** Message: 16:10:05.528: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation] ** Message: 16:10:05.528: Processing model [c2c] ** Message: 16:10:05.528: Bootstrapper processing model [coding2coding] ** Message: 16:10:05.528: Process optimal [optimal:coding2coding] ** Message: 16:10:05.530: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_coding2coding_32_find_32_score.c ** Message: 16:10:06.157: 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_2/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_2/optimal_58_coding2coding_32_find_32_path.c ** Message: 16:10:07.266: 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_2/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_2/optimal_58_coding2coding_32_find_32_region.c ** Message: 16:10:08.315: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_coding2coding_32_find_32_checkpoint.c ** Message: 16:10:10.309: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_coding2coding_32_find_32_path_32_continuation.c ** Message: 16:10:12.942: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_coding2coding_32_find_32_score.o] ** Message: 16:10:12.942: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_coding2coding_32_find_32_score.o ** Message: 16:10:12.953: Adding function [optimal_58_coding2coding_32_find_32_score] ** Message: 16:10:12.953: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_coding2coding_32_find_32_path.o] ** Message: 16:10:12.953: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_coding2coding_32_find_32_path.o ** Message: 16:10:12.963: Adding function [optimal_58_coding2coding_32_find_32_path] ** Message: 16:10:12.963: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_coding2coding_32_find_32_region.o] ** Message: 16:10:12.963: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_coding2coding_32_find_32_region.o ** Message: 16:10:12.973: Adding function [optimal_58_coding2coding_32_find_32_region] ** Message: 16:10:12.973: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_coding2coding_32_find_32_checkpoint.o] ** Message: 16:10:12.973: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_coding2coding_32_find_32_checkpoint.o ** Message: 16:10:12.984: Adding function [optimal_58_coding2coding_32_find_32_checkpoint] ** Message: 16:10:12.984: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_coding2coding_32_find_32_path_32_continuation.o] ** Message: 16:10:12.984: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_coding2coding_32_find_32_path_32_continuation.o ** Message: 16:10:12.995: Adding function [optimal_58_coding2coding_32_find_32_path_32_continuation] ** Message: 16:10:13.015: Process optimal [Terminal [Segment("START"->"match"):[coding2coding]]] ** Message: 16:10:13.018: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/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: 16:10:14.745: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/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: 16:10:16.723: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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: 16:10:16.723: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/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: 16:10:16.738: 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: 16:10:16.738: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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: 16:10:16.738: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/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: 16:10:16.753: 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: 16:10:16.753: Process optimal [Terminal [Segment("match"->"END"):[coding2coding]]] ** Message: 16:10:16.755: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/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: 16:10:17.821: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/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: 16:10:19.126: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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: 16:10:19.126: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/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: 16:10:19.139: 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: 16:10:19.140: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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: 16:10:19.140: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/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: 16:10:19.151: 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: 16:10:19.151: Process optimal [HeuristicJoin:[Segment("match"->"match"):[coding2coding]]] ** Message: 16:10:19.156: 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_2/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_2/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: 16:10:22.104: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/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: 16:10:26.743: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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: 16:10:26.743: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/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: 16:10:26.755: 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: 16:10:26.755: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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: 16:10:26.755: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/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: 16:10:26.767: 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: 16:10:26.768: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.c ** Message: 16:10:27.271: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.c ** Message: 16:10:27.630: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.o] ** Message: 16:10:27.630: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.o ** Message: 16:10:27.644: Adding function [Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded] ** Message: 16:10:27.644: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.o] ** Message: 16:10:27.644: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.o ** Message: 16:10:27.656: Adding function [Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded] ** Message: 16:10:27.656: Processing model [c2g] ** Message: 16:10:27.658: Bootstrapper processing model [coding2genome] ** Message: 16:10:27.658: Process optimal [optimal:coding2genome] ** Message: 16:10:27.662: 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_2/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_2/optimal_58_coding2genome_32_find_32_score.c ** Message: 16:10:29.391: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_coding2genome_32_find_32_path.c ** Message: 16:10:31.318: 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_2/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_2/optimal_58_coding2genome_32_find_32_region.c ** Message: 16:10:33.028: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_coding2genome_32_find_32_checkpoint.c ** Message: 16:10:37.976: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_coding2genome_32_find_32_path_32_continuation.c ** Message: 16:10:43.741: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_coding2genome_32_find_32_score.o] ** Message: 16:10:43.741: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_coding2genome_32_find_32_score.o ** Message: 16:10:43.753: Adding function [optimal_58_coding2genome_32_find_32_score] ** Message: 16:10:43.753: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_coding2genome_32_find_32_path.o] ** Message: 16:10:43.753: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_coding2genome_32_find_32_path.o ** Message: 16:10:43.763: Adding function [optimal_58_coding2genome_32_find_32_path] ** Message: 16:10:43.763: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_coding2genome_32_find_32_region.o] ** Message: 16:10:43.763: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_coding2genome_32_find_32_region.o ** Message: 16:10:43.776: Adding function [optimal_58_coding2genome_32_find_32_region] ** Message: 16:10:43.776: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_coding2genome_32_find_32_checkpoint.o] ** Message: 16:10:43.776: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_coding2genome_32_find_32_checkpoint.o ** Message: 16:10:43.793: Adding function [optimal_58_coding2genome_32_find_32_checkpoint] ** Message: 16:10:43.793: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_coding2genome_32_find_32_path_32_continuation.o] ** Message: 16:10:43.793: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_coding2genome_32_find_32_path_32_continuation.o ** Message: 16:10:43.805: Adding function [optimal_58_coding2genome_32_find_32_path_32_continuation] ** Message: 16:10:43.805: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.c ** Message: 16:10:44.254: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.c ** Message: 16:10:44.922: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.o] ** Message: 16:10:44.922: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.o ** Message: 16:10:44.939: Adding function [Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary] ** Message: 16:10:44.939: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.o] ** Message: 16:10:44.939: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.o ** Message: 16:10:44.957: Adding function [Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary] ** Message: 16:10:44.957: Processing model [cd2g] ** Message: 16:10:44.958: Bootstrapper processing model [cdna2genome] ** Message: 16:10:44.958: Process optimal [optimal:cdna2genome] ** Message: 16:10:44.962: 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_2/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_2/optimal_58_cdna2genome_32_find_32_score.c ** Message: 16:10:48.204: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_cdna2genome_32_find_32_path.c ** Message: 16:10:52.150: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_cdna2genome_32_find_32_region.c ** Message: 16:10:56.059: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_cdna2genome_32_find_32_checkpoint.c ** Message: 16:11:08.082: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_cdna2genome_32_find_32_path_32_continuation.c ** Message: 16:11:29.740: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_cdna2genome_32_find_32_score.o] ** Message: 16:11:29.805: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_cdna2genome_32_find_32_score.o ** Message: 16:11:29.849: Adding function [optimal_58_cdna2genome_32_find_32_score] ** Message: 16:11:29.849: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_cdna2genome_32_find_32_path.o] ** Message: 16:11:29.849: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_cdna2genome_32_find_32_path.o ** Message: 16:11:29.866: Adding function [optimal_58_cdna2genome_32_find_32_path] ** Message: 16:11:29.866: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_cdna2genome_32_find_32_region.o] ** Message: 16:11:29.866: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_cdna2genome_32_find_32_region.o ** Message: 16:11:29.883: Adding function [optimal_58_cdna2genome_32_find_32_region] ** Message: 16:11:29.883: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_cdna2genome_32_find_32_checkpoint.o] ** Message: 16:11:29.883: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_cdna2genome_32_find_32_checkpoint.o ** Message: 16:11:29.897: Adding function [optimal_58_cdna2genome_32_find_32_checkpoint] ** Message: 16:11:29.897: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/optimal_58_cdna2genome_32_find_32_path_32_continuation.o] ** Message: 16:11:29.897: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/optimal_58_cdna2genome_32_find_32_path_32_continuation.o ** Message: 16:11:29.914: Adding function [optimal_58_cdna2genome_32_find_32_path_32_continuation] ** Message: 16:11:29.916: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.c ** Message: 16:11:31.042: Compiling codegen: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/struct -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/general -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sequence -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/model -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/comparison -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/c4 -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/bsdp -I/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/src/sdp -o /wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.c ** Message: 16:11:31.635: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o] ** Message: 16:11:31.635: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o ** Message: 16:11:31.650: Adding function [Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary] ** Message: 16:11:31.650: Adding: [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o] ** Message: 16:11:31.650: Adding object file [/wrkdirs/usr/ports/biology/exonerate/work/exonerate-2.4.0/codegen/amd64_45_portbld_45_freebsd13_46_2/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_2/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o ** Message: 16:11:31.668: Adding function [Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary] ** Message: 16:11:31.668: 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: 16:11:32.060: Adding: [c4_model_lookup.o] ** Message: 16:11:32.060: Adding object file [c4_model_lookup.o] to archive ar -Sq c4_model_archive.a c4_model_lookup.o ** Message: 16:11:32.080: Indexing archive [c4_model_archive.a] ranlib c4_model_archive.a ** Message: 16:11:32.101: Done ** Message: 16:11:32.101: 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-freebsd13.2\"" -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] if((macro[i] == '%')){ ~~~~~~~~~^~~~~~ ../../src/c4/viterbi.c:877:22: note: remove extraneous parentheses around the comparison to silence this warning if((macro[i] == '%')){ ~ ^ ~ ../../src/c4/viterbi.c:877:22: note: use '=' to turn this equality comparison into an assignment 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-freebsd13.2\"" -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 -fstack-protector-strong -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-freebsd13.2\"" -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] g_strup(primer_a); ^ /usr/local/include/glib-2.0/glib/gstrfuncs.h:276:1: note: 'g_strup' has been explicitly marked deprecated here GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #define G_DEPRECATED __attribute__((__deprecated__)) ^ ipcress.c:265:9: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] g_strup(primer_b); ^ /usr/local/include/glib-2.0/glib/gstrfuncs.h:276:1: note: 'g_strup' has been explicitly marked deprecated here GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #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 -fstack-protector-strong -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-freebsd13.2\"" -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] g_string_sprintfa(str, "hspset: %d", index_hsp_set->target_id); ^ /usr/local/include/glib-2.0/glib/gstring.h:292:51: note: expanded from macro 'g_string_sprintfa' #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' #define GLIB_DEPRECATED_MACRO_IN_2_26_FOR(f) GLIB_DEPRECATED_MACRO_FOR (f) ^ /usr/local/include/glib-2.0/glib/gmacros.h:1300:3: note: expanded from macro 'GLIB_DEPRECATED_MACRO_FOR' _GLIB_GNUC_DO_PRAGMA(GCC warning G_STRINGIFY (Deprecated pre-processor symbol: replace with #f)) ^ /usr/local/include/glib-2.0/glib/gmacros.h:1297:33: note: expanded from macro '_GLIB_GNUC_DO_PRAGMA' #define _GLIB_GNUC_DO_PRAGMA(x) _Pragma(G_STRINGIFY (x)) ^ :3:6: note: expanded from here 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] g_string_sprintfa(str, " %d %d %d", ^ /usr/local/include/glib-2.0/glib/gstring.h:292:51: note: expanded from macro 'g_string_sprintfa' #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' #define GLIB_DEPRECATED_MACRO_IN_2_26_FOR(f) GLIB_DEPRECATED_MACRO_FOR (f) ^ /usr/local/include/glib-2.0/glib/gmacros.h:1300:3: note: expanded from macro 'GLIB_DEPRECATED_MACRO_FOR' _GLIB_GNUC_DO_PRAGMA(GCC warning G_STRINGIFY (Deprecated pre-processor symbol: replace with #f)) ^ /usr/local/include/glib-2.0/glib/gmacros.h:1297:33: note: expanded from macro '_GLIB_GNUC_DO_PRAGMA' #define _GLIB_GNUC_DO_PRAGMA(x) _Pragma(G_STRINGIFY (x)) ^ :8:6: note: expanded from here 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] g_string_sprintfa(str, "\n"); ^ /usr/local/include/glib-2.0/glib/gstring.h:292:51: note: expanded from macro 'g_string_sprintfa' #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' #define GLIB_DEPRECATED_MACRO_IN_2_26_FOR(f) GLIB_DEPRECATED_MACRO_FOR (f) ^ /usr/local/include/glib-2.0/glib/gmacros.h:1300:3: note: expanded from macro 'GLIB_DEPRECATED_MACRO_FOR' _GLIB_GNUC_DO_PRAGMA(GCC warning G_STRINGIFY (Deprecated pre-processor symbol: replace with #f)) ^ /usr/local/include/glib-2.0/glib/gmacros.h:1297:33: note: expanded from macro '_GLIB_GNUC_DO_PRAGMA' #define _GLIB_GNUC_DO_PRAGMA(x) _Pragma(G_STRINGIFY (x)) ^ :13:6: note: expanded from here 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] if(!msg[msg_len-1] == '\n') ^ ~~ exonerate-server.c:655:8: note: add parentheses after the '!' to evaluate the comparison first if(!msg[msg_len-1] == '\n') ^ ( ) exonerate-server.c:655:8: note: add parentheses around left hand side expression to silence this warning 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] 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] 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] 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] 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 -fstack-protector-strong -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 -fstack-protector-strong -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 -fstack-protector-strong -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 -fstack-protector-strong -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 -fstack-protector-strong -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] comp = g_strcasecmp; ^ /usr/local/include/glib-2.0/glib/gstrfuncs.h:267:1: note: 'g_strcasecmp' has been explicitly marked deprecated here GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #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 -fstack-protector-strong -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 -fstack-protector-strong -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] 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 GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #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 -fstack-protector-strong -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 -fstack-protector-strong -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 -fstack-protector-strong -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 -fstack-protector-strong -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 -fstack-protector-strong -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 -fstack-protector-strong -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 -fstack-protector-strong -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] 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 GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #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 -fstack-protector-strong -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 -fstack-protector-strong -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] 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 -fstack-protector-strong -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] 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 GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #define G_DEPRECATED __attribute__((__deprecated__)) ^ fastasort.c:132:14: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 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 GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #define G_DEPRECATED __attribute__((__deprecated__)) ^ fastasort.c:134:14: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 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 GLIB_DEPRECATED ^ /usr/local/include/glib-2.0/glib/glib-visibility.h:30:25: note: expanded from macro 'GLIB_DEPRECATED' #define GLIB_DEPRECATED G_DEPRECATED _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1263:37: note: expanded from macro 'G_DEPRECATED' #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 -fstack-protector-strong -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] 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 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' #define GLIB_DEPRECATED_FOR(f) G_DEPRECATED_FOR(f) _GLIB_EXTERN ^ /usr/local/include/glib-2.0/glib/gmacros.h:1273:44: note: expanded from macro 'G_DEPRECATED_FOR' #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 -fstack-protector-strong -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 -fstack-protector-strong -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 -fstack-protector-strong -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 -fstack-protector-strong -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 -fstack-protector-strong -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 -fstack-protector-strong -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 -fstack-protector-strong -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=2024-04-03T16:05:54+0000' 'PKG_NOTE_ports_top_git_hash=c2c35d895e' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=2044d70d1f' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.99.20240122_1' 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 Wed Apr 3 17:11:49 BST 2024 build time: 00:05:55