=>> Building biology/augustus build started at Fri Mar 13 01:00:40 EDT 2026 port directory: /usr/ports/biology/augustus package name: augustus-gene-prediction-3.5.0_17 building for: FreeBSD pkg.DaveG.ca 14.4-RELEASE FreeBSD 14.4-RELEASE 1404000 amd64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1209 Feb 17 19:06 /usr/ports/biology/augustus/Makefile Ports top last git commit: 26b198eb3ee3 Ports top unclean checkout: no Port dir last git commit: 2e4f3d1acf81 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1404000 Job Id: 10 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1404000 UNAME_v=FreeBSD 14.4-RELEASE 1404000 UNAME_r=14.4-RELEASE BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/freebsd_14_4_x64-HEAD-ALL/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=tmux-256color OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/freebsd_14_4_x64-HEAD-ALL/10/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_14_4_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_14_4_x64-HEAD-ALL/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=/usr/local/bin/gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 PYTHON="/usr/local/bin/python3.11" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/augustus/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/augustus/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/augustus/work/.cache HOME=/wrkdirs/usr/ports/biology/augustus/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/augustus/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/augustus/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CMAKE_PREFIX_PATH="/usr/local" --End CONFIGURE_ENV-- --MAKE_ENV-- PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/augustus/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/augustus/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/augustus/work/.cache HOME=/wrkdirs/usr/ports/biology/augustus/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/augustus/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/augustus/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -L/usr/local/lib/mysql -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 " CXXSTD=c++14 BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- PYTHON_INCLUDEDIR=include/python3.11 PYTHON_LIBDIR=lib/python3.11 PYTHON_PLATFORM=freebsd14 PYTHON_SITELIBDIR=lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_BASESUFFIX=311 PYTHON_TAG=.cpython-311 PYTHON_SOABI=.cpython-311 PYTHON_VER=3.11 PYTHON_BASEVER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" OSREL=14.4 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.42.0 PERL_VER=5.42 PERL5_MAN1=lib/perl5/site_perl/man/man1 PERL5_MAN3=lib/perl5/site_perl/man/man3 SITE_PERL=lib/perl5/site_perl SITE_ARCH=lib/perl5/site_perl/mach/5.42 DOCSDIR="share/doc/augustus" EXAMPLESDIR="share/examples/augustus" DATADIR="share/augustus" WWWDIR="www/augustus" ETCDIR="etc/augustus" --End PLIST_SUB-- --SUB_LIST-- PYTHON_INCLUDEDIR=/usr/local/include/python3.11 PYTHON_LIBDIR=/usr/local/lib/python3.11 PYTHON_PLATFORM=freebsd14 PYTHON_SITELIBDIR=/usr/local/lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_BASESUFFIX=311 PYTHON_TAG=.cpython-311 PYTHON_SOABI=.cpython-311 PYTHON_VER=3.11 PYTHON_BASEVER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/augustus DOCSDIR=/usr/local/share/doc/augustus EXAMPLESDIR=/usr/local/share/examples/augustus WWWDIR=/usr/local/www/augustus ETCDIR=/usr/local/etc/augustus --End SUB_LIST-- ---Begin make.conf--- DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited pipebuf (-y) 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 ===> augustus-gene-prediction-3.5.0_17 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.6.2.pkg [pkg.DaveG.ca] Installing pkg-2.6.2... [pkg.DaveG.ca] Extracting pkg-2.6.2: .......... done ===> augustus-gene-prediction-3.5.0_17 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of augustus-gene-prediction-3.5.0_17 =========================================================================== =================================================== ===== 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 augustus-gene-prediction-3.5.0_17 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by augustus-gene-prediction-3.5.0_17 for building => SHA256 Checksum OK for Gaius-Augustus-Augustus-v3.5.0_GH0.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 augustus-gene-prediction-3.5.0_17 for building ===> Extracting for augustus-gene-prediction-3.5.0_17 => SHA256 Checksum OK for Gaius-Augustus-Augustus-v3.5.0_GH0.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 augustus-gene-prediction-3.5.0_17 ===> Applying FreeBSD patches for augustus-gene-prediction-3.5.0_17 from /usr/ports/biology/augustus/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> augustus-gene-prediction-3.5.0_17 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [pkg.DaveG.ca] Installing gmake-4.4.1... [pkg.DaveG.ca] `-- Installing gettext-runtime-0.26... [pkg.DaveG.ca] | `-- Installing indexinfo-0.3.1_1... [pkg.DaveG.ca] | `-- Extracting indexinfo-0.3.1_1: . done [pkg.DaveG.ca] `-- Extracting gettext-runtime-0.26: .......... done [pkg.DaveG.ca] Extracting gmake-4.4.1: .......... done ===> augustus-gene-prediction-3.5.0_17 depends on package: gmake>=4.4.1 - found ===> Returning to build of augustus-gene-prediction-3.5.0_17 ===> augustus-gene-prediction-3.5.0_17 depends on file: /usr/local/bin/python3.11 - not found ===> Installing existing package /packages/All/python311-3.11.15.pkg [pkg.DaveG.ca] Installing python311-3.11.15... [pkg.DaveG.ca] `-- Installing libffi-3.5.1... [pkg.DaveG.ca] `-- Extracting libffi-3.5.1: .......... done [pkg.DaveG.ca] `-- Installing mpdecimal-4.0.1... [pkg.DaveG.ca] `-- Extracting mpdecimal-4.0.1: .......... done [pkg.DaveG.ca] `-- Installing readline-8.3.3... [pkg.DaveG.ca] `-- Extracting readline-8.3.3: .......... done [pkg.DaveG.ca] Extracting python311-3.11.15: .......... done ===== Message from python311-3.11.15: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py311-gdbm databases/py-gdbm@py311 py311-sqlite3 databases/py-sqlite3@py311 py311-tkinter x11-toolkits/py-tkinter@py311 ===> augustus-gene-prediction-3.5.0_17 depends on file: /usr/local/bin/python3.11 - found ===> Returning to build of augustus-gene-prediction-3.5.0_17 ===> augustus-gene-prediction-3.5.0_17 depends on package: perl5>=5.42.r<5.43 - not found ===> Installing existing package /packages/All/perl5-5.42.0_1.pkg [pkg.DaveG.ca] Installing perl5-5.42.0_1... [pkg.DaveG.ca] Extracting perl5-5.42.0_1: .......... done ===> augustus-gene-prediction-3.5.0_17 depends on package: perl5>=5.42.r<5.43 - found ===> Returning to build of augustus-gene-prediction-3.5.0_17 ===> augustus-gene-prediction-3.5.0_17 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg.DaveG.ca] Installing ccache-3.7.12_8... [pkg.DaveG.ca] Extracting ccache-3.7.12_8: ......... done Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for clang create symlink for clang (world) create symlink for clang++ create symlink for clang++ (world) ===== Message from ccache-3.7.12_8: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. ===> augustus-gene-prediction-3.5.0_17 depends on file: /usr/local/bin/ccache - found ===> Returning to build of augustus-gene-prediction-3.5.0_17 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> augustus-gene-prediction-3.5.0_17 depends on shared library: libbamtools.so - not found ===> Installing existing package /packages/All/bamtools-2.5.3.pkg [pkg.DaveG.ca] Installing bamtools-2.5.3... [pkg.DaveG.ca] `-- Installing jsoncpp-1.9.6_1... [pkg.DaveG.ca] `-- Extracting jsoncpp-1.9.6_1: .......... done [pkg.DaveG.ca] Extracting bamtools-2.5.3: .......... done ===> augustus-gene-prediction-3.5.0_17 depends on shared library: libbamtools.so - found (/usr/local/lib/libbamtools.so) ===> Returning to build of augustus-gene-prediction-3.5.0_17 ===> augustus-gene-prediction-3.5.0_17 depends on shared library: libboost_iostreams.so - not found ===> Installing existing package /packages/All/boost-libs-1.89.0_2.pkg [pkg.DaveG.ca] Installing boost-libs-1.89.0_2... [pkg.DaveG.ca] `-- Installing icu-76.1,1... [pkg.DaveG.ca] `-- Extracting icu-76.1,1: .......... done [pkg.DaveG.ca] `-- Installing zstd-1.5.7_1... [pkg.DaveG.ca] `-- Extracting zstd-1.5.7_1: .......... done [pkg.DaveG.ca] Extracting boost-libs-1.89.0_2: .......... done ===== Message from boost-libs-1.89.0_2: -- You have built the Boost library with thread support. Don't forget to add -pthread to your linker options when linking your code. ===> augustus-gene-prediction-3.5.0_17 depends on shared library: libboost_iostreams.so - found (/usr/local/lib/libboost_iostreams.so) ===> Returning to build of augustus-gene-prediction-3.5.0_17 ===> augustus-gene-prediction-3.5.0_17 depends on shared library: libcolamd.so - not found ===> Installing existing package /packages/All/suitesparse-colamd-3.3.5.pkg [pkg.DaveG.ca] Installing suitesparse-colamd-3.3.5... [pkg.DaveG.ca] `-- Installing gcc14-14.2.0_4... [pkg.DaveG.ca] | `-- Installing binutils-2.44,1... [pkg.DaveG.ca] | `-- Extracting binutils-2.44,1: .......... done [pkg.DaveG.ca] | `-- Installing gmp-6.3.0... [pkg.DaveG.ca] | `-- Extracting gmp-6.3.0: .......... done [pkg.DaveG.ca] | `-- Installing mpc-1.3.1_1... [pkg.DaveG.ca] | | `-- Installing mpfr-4.2.2,1... [pkg.DaveG.ca] | | `-- Extracting mpfr-4.2.2,1: .......... done [pkg.DaveG.ca] | `-- Extracting mpc-1.3.1_1: ...... done [pkg.DaveG.ca] `-- Extracting gcc14-14.2.0_4: .......... done create symlink for gcc14 create symlink for gcc14 (world) create symlink for g++14 create symlink for g++14 (world) create symlink for cpp14 create symlink for cpp14 (world) [pkg.DaveG.ca] `-- Installing suitesparse-config-7.12.2... [pkg.DaveG.ca] | `-- Installing openblas-0.3.30,2... [pkg.DaveG.ca] | `-- Extracting openblas-0.3.30,2: .......... done [pkg.DaveG.ca] `-- Extracting suitesparse-config-7.12.2: .......... done [pkg.DaveG.ca] Extracting suitesparse-colamd-3.3.5: .......... done ===== Message from gcc14-14.2.0_4: -- To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc14 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> augustus-gene-prediction-3.5.0_17 depends on shared library: libcolamd.so - found (/usr/local/lib/libcolamd.so) ===> Returning to build of augustus-gene-prediction-3.5.0_17 ===> augustus-gene-prediction-3.5.0_17 depends on shared library: libgsl.so - not found ===> Installing existing package /packages/All/gsl-2.8.pkg [pkg.DaveG.ca] Installing gsl-2.8... [pkg.DaveG.ca] Extracting gsl-2.8: .......... done ===> augustus-gene-prediction-3.5.0_17 depends on shared library: libgsl.so - found (/usr/local/lib/libgsl.so) ===> Returning to build of augustus-gene-prediction-3.5.0_17 ===> augustus-gene-prediction-3.5.0_17 depends on shared library: libhts.so - not found ===> Installing existing package /packages/All/htslib-1.22.pkg [pkg.DaveG.ca] Installing htslib-1.22... [pkg.DaveG.ca] `-- Installing curl-8.17.0... [pkg.DaveG.ca] | `-- Installing brotli-1.2.0,1... [pkg.DaveG.ca] | `-- Extracting brotli-1.2.0,1: .......... done [pkg.DaveG.ca] | `-- Installing libidn2-2.3.8... [pkg.DaveG.ca] | | `-- Installing libunistring-1.4.2... [pkg.DaveG.ca] | | `-- Extracting libunistring-1.4.2: .......... done [pkg.DaveG.ca] | `-- Extracting libidn2-2.3.8: .......... done [pkg.DaveG.ca] | `-- Installing libnghttp2-1.68.0... [pkg.DaveG.ca] | `-- Extracting libnghttp2-1.68.0: ....... done [pkg.DaveG.ca] | `-- Installing libpsl-0.21.5_2... [pkg.DaveG.ca] | `-- Extracting libpsl-0.21.5_2: ........ done [pkg.DaveG.ca] | `-- Installing libssh2-1.11.1,3... [pkg.DaveG.ca] | `-- Extracting libssh2-1.11.1,3: .......... done [pkg.DaveG.ca] `-- Extracting curl-8.17.0: .......... done [pkg.DaveG.ca] `-- Installing libdeflate-1.25... [pkg.DaveG.ca] `-- Extracting libdeflate-1.25: .......... done [pkg.DaveG.ca] Extracting htslib-1.22: .......... done ===> augustus-gene-prediction-3.5.0_17 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> Returning to build of augustus-gene-prediction-3.5.0_17 ===> augustus-gene-prediction-3.5.0_17 depends on shared library: liblpsolve55.so - not found ===> Installing existing package /packages/All/lp_solve-5.5.2.5_1.pkg [pkg.DaveG.ca] Installing lp_solve-5.5.2.5_1... [pkg.DaveG.ca] Extracting lp_solve-5.5.2.5_1: .......... done ===> augustus-gene-prediction-3.5.0_17 depends on shared library: liblpsolve55.so - found (/usr/local/lib/liblpsolve55.so) ===> Returning to build of augustus-gene-prediction-3.5.0_17 ===> augustus-gene-prediction-3.5.0_17 depends on shared library: libmysqlpp.so - not found ===> Installing existing package /packages/All/mysql++-3.3.0.pkg [pkg.DaveG.ca] Installing mysql++-3.3.0... [pkg.DaveG.ca] `-- Installing mysql80-client-8.0.45... [pkg.DaveG.ca] | `-- Installing cyrus-sasl-2.1.28_5... *** Added group `cyrus' (id 60) *** Added user `cyrus' (id 60) [pkg.DaveG.ca] | `-- Extracting cyrus-sasl-2.1.28_5: .......... done [pkg.DaveG.ca] | `-- Installing groff-1.24.0... [pkg.DaveG.ca] | | `-- Installing libiconv-1.18_1... [pkg.DaveG.ca] | | `-- Extracting libiconv-1.18_1: .......... done [pkg.DaveG.ca] | | `-- Installing psutils-1.17_6... [pkg.DaveG.ca] | | `-- Installing libpaper-1.1.28_1... [pkg.DaveG.ca] | | `-- Extracting libpaper-1.1.28_1: .......... done [pkg.DaveG.ca] | | `-- Extracting psutils-1.17_6: .......... done [pkg.DaveG.ca] | | `-- Installing uchardet-0.0.8_1... [pkg.DaveG.ca] | | `-- Extracting uchardet-0.0.8_1: .......... done [pkg.DaveG.ca] | `-- Extracting groff-1.24.0: .......... done [pkg.DaveG.ca] | `-- Installing hidapi-0.15.0... [pkg.DaveG.ca] | `-- Extracting hidapi-0.15.0: .......... done [pkg.DaveG.ca] | `-- Installing libedit-3.1.20251016_1,1... [pkg.DaveG.ca] | `-- Extracting libedit-3.1.20251016_1,1: .......... done [pkg.DaveG.ca] | `-- Installing libevent-2.1.12... [pkg.DaveG.ca] | `-- Extracting libevent-2.1.12: .......... done [pkg.DaveG.ca] | `-- Installing libfido2-1.16.0... [pkg.DaveG.ca] | | `-- Installing libcbor-0.13.0... [pkg.DaveG.ca] | | `-- Extracting libcbor-0.13.0: .......... done [pkg.DaveG.ca] | `-- Extracting libfido2-1.16.0: .......... done [pkg.DaveG.ca] | `-- Installing liblz4-1.10.0_2,1... [pkg.DaveG.ca] | `-- Extracting liblz4-1.10.0_2,1: .......... done [pkg.DaveG.ca] | `-- Installing libunwind-20250904... [pkg.DaveG.ca] | `-- Extracting libunwind-20250904: .......... done [pkg.DaveG.ca] | `-- Installing openldap26-client-2.6.12... [pkg.DaveG.ca] | `-- Extracting openldap26-client-2.6.12: .......... done [pkg.DaveG.ca] `-- Extracting mysql80-client-8.0.45: .......... done [pkg.DaveG.ca] Extracting mysql++-3.3.0: .......... done ===== Message from cyrus-sasl-2.1.28_5: -- You can use sasldb2 for authentication, to add users use: saslpasswd2 -c username If you want to enable SMTP AUTH with the system Sendmail, read Sendmail.README NOTE: This port has been compiled with a default pwcheck_method of auxprop. If you want to authenticate your user by /etc/passwd, PAM or LDAP, install ports/security/cyrus-sasl2-saslauthd and set sasl_pwcheck_method to saslauthd after installing the Cyrus-IMAPd 2.X port. You should also check the /usr/local/lib/sasl2/*.conf files for the correct pwcheck_method. If you want to use GSSAPI mechanism, install ports/security/cyrus-sasl2-gssapi. If you want to use SRP mechanism, install ports/security/cyrus-sasl2-srp. If you want to use LDAP auxprop plugin, install ports/security/cyrus-sasl2-ldapdb. ===== Message from groff-1.24.0: -- In order to be able to use the html driver, you need to install the following packages: - ghostscript - netpbm ===== Message from openldap26-client-2.6.12: -- The OpenLDAP client package has been successfully installed. Edit /usr/local/etc/openldap/ldap.conf to change the system-wide client defaults. Try `man ldap.conf' and visit the OpenLDAP FAQ-O-Matic at http://www.OpenLDAP.org/faq/index.cgi?file=3 for more information. ===== Message from mysql80-client-8.0.45: -- This is the mysql CLIENT without the server. for complete server and client, please install databases/mysql80-server ===> augustus-gene-prediction-3.5.0_17 depends on shared library: libmysqlpp.so - found (/usr/local/lib/libmysqlpp.so) ===> Returning to build of augustus-gene-prediction-3.5.0_17 ===> augustus-gene-prediction-3.5.0_17 depends on shared library: libmysqlclient.so.21 - found (/usr/local/lib/mysql/libmysqlclient.so.21) ===> augustus-gene-prediction-3.5.0_17 depends on shared library: libsqlite3.so - not found ===> Installing existing package /packages/All/sqlite3-3.50.4_2,1.pkg [pkg.DaveG.ca] Installing sqlite3-3.50.4_2,1... [pkg.DaveG.ca] Extracting sqlite3-3.50.4_2,1: .......... done ===> augustus-gene-prediction-3.5.0_17 depends on shared library: libsqlite3.so - found (/usr/local/lib/libsqlite3.so) ===> Returning to build of augustus-gene-prediction-3.5.0_17 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for augustus-gene-prediction-3.5.0_17 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for augustus-gene-prediction-3.5.0_17 mkdir -p bin mkdir -p bin cd src && /usr/local/bin/gmake cd auxprogs && /usr/local/bin/gmake gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/augustus/work/Augustus-3.5.0/src' gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/augustus/work/Augustus-3.5.0/auxprogs' cd aln2wig; make; make[2]: Entering directory '/wrkdirs/usr/ports/biology/augustus/work/Augustus-3.5.0/auxprogs/aln2wig' cc -isystem /usr/local/include -Wall -Wno-sign-compare -ansi -pedantic -O2 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c aln2wig.c c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o genbank.o genbank.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o properties.o properties.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o pp_profile.o pp_profile.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o pp_hitseq.o pp_hitseq.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o pp_scoring.o pp_scoring.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o statemodel.o statemodel.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o namgene.o namgene.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o types.o types.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o gene.o gene.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o evaluation.o evaluation.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o motif.o motif.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o geneticcode.o geneticcode.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o hints.o hints.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o extrinsicinfo.o extrinsicinfo.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o projectio.o projectio.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o intronmodel.o intronmodel.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o exonmodel.o exonmodel.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o igenicmodel.o igenicmodel.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o utrmodel.o utrmodel.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o merkmal.o merkmal.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o vitmatrix.o vitmatrix.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o lldouble.o lldouble.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o mea.o mea.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o graph.o graph.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o meaPath.o meaPath.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o exoncand.o exoncand.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o randseqaccess.o randseqaccess.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o fasta.o fasta.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o ncmodel.o ncmodel.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o parser/parse.o parser/parse.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o scanner/lex.o scanner/lex.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o genomicMSA.o genomicMSA.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o geneMSA.o geneMSA.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o contTimeMC.o contTimeMC.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o codonevo.o codonevo.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o compgenepred.o compgenepred.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o phylotree.o phylotree.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o orthograph.o orthograph.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o orthoexon.o orthoexon.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o alignment.o alignment.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o speciesgraph.o speciesgraph.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o codonMSA.o codonMSA.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o train_logReg_param.o train_logReg_param.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o tokenizer.o tokenizer.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o sqliteDB.o sqliteDB.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o commontrain.o commontrain.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o igenictrain.o igenictrain.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o introntrain.o introntrain.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o exontrain.o exontrain.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o utrtrain.o utrtrain.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o dummy.o dummy.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -L/usr/local/lib/mysql -L/usr/local/lib -o prepareAlign pp_prepare_align.cc cc -isystem /usr/local/include -Wall -Wno-sign-compare -ansi -pedantic -O2 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -L/usr/local/lib/mysql -L/usr/local/lib -o aln2wig aln2wig.o c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o pp_fastBlockSearcher.o pp_fastBlockSearcher.cc echo "-Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE" > cxxflags mkdir -p ../../bin cp -f aln2wig ../../bin make[2]: Leaving directory '/wrkdirs/usr/ports/biology/augustus/work/Augustus-3.5.0/auxprogs/aln2wig' cd bam2hints; make; make[2]: Entering directory '/wrkdirs/usr/ports/biology/augustus/work/Augustus-3.5.0/auxprogs/bam2hints' c++ -isystem /usr/local/include -Wall -O3 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I/usr/include/bamtools -c bam2hints.cc grammar:245:13: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation] 245 | return elementPtr->d_action; | ^ grammar:243:9: note: previous statement is here 243 | if (d_debug__) | ^ parser/parse.cc:65:16: warning: unused variable 'author' [-Wunused-const-variable] 65 | char const author[] = "Frank B. Brokken (f.b.brokken@rug.nl)"; | ^~~~~~ 2 warnings generated. cp -f prepareAlign ../bin/ bam2hints.cc:627:12: warning: variable 'Line' set but not used [-Wunused-but-set-variable] 627 | long int Line = 0; // line count | ^ 1 warning generated. c++ -isystem /usr/local/include -Wall -O3 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -L/usr/local/lib/mysql -L/usr/local/lib -L/usr/lib -Wl,-rpath,/usr/lib -I/usr/include/bamtools -o bam2hints bam2hints.o -lbamtools -lz mkdir -p ../../bin cp -f bam2hints ../../bin make[2]: Leaving directory '/wrkdirs/usr/ports/biology/augustus/work/Augustus-3.5.0/auxprogs/bam2hints' cd compileSpliceCands; make; make[2]: Entering directory '/wrkdirs/usr/ports/biology/augustus/work/Augustus-3.5.0/auxprogs/compileSpliceCands' cc -isystem /usr/local/include -Wall -pedantic -ansi -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c compileSpliceCands.c cc -Wall -pedantic -ansi -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -c -o list.o list.c compileSpliceCands.c:38:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 38 | void printOomError() | ^ | void 1 warning generated. cc -isystem /usr/local/include -Wall -pedantic -ansi -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -L/usr/local/lib/mysql -L/usr/local/lib -o compileSpliceCands compileSpliceCands.o list.o cp -f compileSpliceCands ../../bin/compileSpliceCands make[2]: Leaving directory '/wrkdirs/usr/ports/biology/augustus/work/Augustus-3.5.0/auxprogs/compileSpliceCands' cd filterBam; make; make[2]: Entering directory '/wrkdirs/usr/ports/biology/augustus/work/Augustus-3.5.0/auxprogs/filterBam' (cd src;make) make[3]: Entering directory '/wrkdirs/usr/ports/biology/augustus/work/Augustus-3.5.0/auxprogs/filterBam/src' c++ -isystem /usr/local/include -Wall -Wextra -Wpedantic -std=c++11 -O3 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I./headers -I/usr/include/bamtools -c filterBam.cc c++ -isystem /usr/local/include -Wall -Wextra -Wpedantic -std=c++11 -O3 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I./headers -I/usr/include/bamtools -c functions/initOptions.cc c++ -isystem /usr/local/include -Wall -Wextra -Wpedantic -std=c++11 -O3 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I./headers -I/usr/include/bamtools -c functions/printElapsedTime.cc c++ -isystem /usr/local/include -Wall -Wextra -Wpedantic -std=c++11 -O3 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I./headers -I/usr/include/bamtools -c functions/MatePairs.cc c++ -isystem /usr/local/include -Wall -Wextra -Wpedantic -std=c++11 -O3 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I./headers -I/usr/include/bamtools -c functions/PairednessCoverage.cc c++ -isystem /usr/local/include -Wall -Wextra -Wpedantic -std=c++11 -O3 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I./headers -I/usr/include/bamtools -c BamToolsAccess.cc In file included from alignment.cc:8: ../include/alignment.hh:238:89: warning: binding reference member 'a' to stack allocated parameter 'a_' [-Wdangling-field] 238 | IdxSortCriterion(vector const a_, size_t speciesIdx) : s(speciesIdx), a(a_) {}; | ^~ ../include/alignment.hh:253:31: note: reference member declared here 253 | vector const &a; | ^ 1 warning generated. In file included from phylotree.cc:12: ../include/phylotree.hh:54:10: warning: private field 'label' is not used [-Wunused-private-field] 54 | bool label; | ^ 1 warning generated. train_logReg_param.cc:490:3: warning: 'random_shuffle> *>>' is deprecated [-Wdeprecated-declarations] 490 | random_shuffle ( samples->begin(), samples->end() ); | ^ /usr/include/c++/v1/__algorithm/shuffle.h:95:23: note: 'random_shuffle> *>>' has been explicitly marked deprecated here 95 | _LIBCPP_HIDE_FROM_ABI _LIBCPP_DEPRECATED_IN_CXX14 void | ^ /usr/include/c++/v1/__config:742:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX14' 742 | # define _LIBCPP_DEPRECATED_IN_CXX14 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 1 warning generated. mea.cc:326:29: warning: variable 'codlength' set but not used [-Wunused-but-set-variable] 326 | int transStart, transEnd, codlength = 0; | ^ 1 warning generated. exonmodel.cc:1995:2: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation] 1995 | Double seqProb = 1; | ^ exonmodel.cc:1986:5: note: previous statement is here 1986 | if (!(right-left+1 == Constant::et_coding_len)) | ^ 1 warning generated. namgene.cc:270:8: warning: variable 'deletedSubmaps' set but not used [-Wunused-but-set-variable] 270 | int deletedSubmaps=0; | ^ namgene.cc:1510:10: warning: variable 'allReachable' set but not used [-Wunused-but-set-variable] 1510 | bool allReachable; | ^ 2 warnings generated. c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -L/usr/local/lib/mysql -L/usr/local/lib -I../include -I/usr/include/lpsolve -I/usr/include/mysql -o fastBlockSearch fastBlockSearch.cc pp_fastBlockSearcher.o types.o properties.o geneticcode.o pp_profile.o lldouble.o -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lboost_serialization -lmysqlclient -lmysqlpp -lsqlite3 c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -L/usr/local/lib/mysql -L/usr/local/lib -I../include -I/usr/include/lpsolve -I/usr/include/mysql -o pp_simScore pp_simscore.cc fasta.o types.o properties.o geneticcode.o pp_profile.o lldouble.o -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lboost_serialization -lmysqlclient -lmysqlpp -lsqlite3 c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -L/usr/local/lib/mysql -L/usr/local/lib -I../include -I/usr/include/lpsolve -I/usr/include/mysql -o load2db load2db.cc fasta.o hints.o types.o properties.o lldouble.o -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lboost_serialization -lmysqlclient -lmysqlpp -lsqlite3 c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -L/usr/local/lib/mysql -L/usr/local/lib -I../include -I/usr/include/lpsolve -I/usr/include/mysql -o load2sqlitedb load2sqlitedb.cc fasta.o hints.o types.o properties.o lldouble.o sqliteDB.o -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lboost_serialization -lmysqlclient -lmysqlpp -lsqlite3 In file included from codonevo.cc:10: In file included from ../include/geneMSA.hh:12: ../include/alignment.hh:238:89: warning: binding reference member 'a' to stack allocated parameter 'a_' [-Wdangling-field] 238 | IdxSortCriterion(vector const a_, size_t speciesIdx) : s(speciesIdx), a(a_) {}; | ^~ ../include/alignment.hh:253:31: note: reference member declared here 253 | vector const &a; | ^ 1 warning generated. In file included from orthograph.cc:10: In file included from ../include/orthograph.hh:15: In file included from ../include/geneMSA.hh:12: ../include/alignment.hh:238:89: warning: binding reference member 'a' to stack allocated parameter 'a_' [-Wdangling-field] 238 | IdxSortCriterion(vector const a_, size_t speciesIdx) : s(speciesIdx), a(a_) {}; | ^~ ../include/alignment.hh:253:31: note: reference member declared here 253 | vector const &a; | ^ 1 warning generated. extrinsicinfo.cc:918:9: warning: variable 'grpcount' set but not used [-Wunused-but-set-variable] 918 | int grpcount = 0, hintcount=0; | ^ extrinsicinfo.cc:918:23: warning: variable 'hintcount' set but not used [-Wunused-but-set-variable] 918 | int grpcount = 0, hintcount=0; | ^ extrinsicinfo.cc:1079:9: warning: variable 'numIncompat' set but not used [-Wunused-but-set-variable] 1079 | int numIncompat = 0, numWeakerThan = 0, numEqual = 0; | ^ extrinsicinfo.cc:1079:26: warning: variable 'numWeakerThan' set but not used [-Wunused-but-set-variable] 1079 | int numIncompat = 0, numWeakerThan = 0, numEqual = 0; | ^ extrinsicinfo.cc:1079:45: warning: variable 'numEqual' set but not used [-Wunused-but-set-variable] 1079 | int numIncompat = 0, numWeakerThan = 0, numEqual = 0; | ^ extrinsicinfo.cc:1115:9: warning: variable 'numTrashy' set but not used [-Wunused-but-set-variable] 1115 | int numTrashy=0; | ^ 6 warnings generated. pp_simscore.cc:870:21: warning: unused variable 'count_miss' [-Wunused-variable] 870 | pair count_miss; | ^~~~~~~~~~ cp -f load2sqlitedb ../bin/ load2db.cc:196:17: warning: result of comparison of constant -1 with expression of type 'FeatureType' is always true [-Wtautological-constant-out-of-range-compare] 196 | if(f.type != -1){ | ~~~~~~ ^ ~~ filterBam.cc:539:10: warning: variable 'nKeys' set but not used [-Wunused-but-set-variable] 539 | size_t nKeys = 1; | ^ 1 warning generated. c++ -isystem /usr/local/include -Wall -Wextra -Wpedantic -std=c++11 -O3 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -L/usr/local/lib/mysql -L/usr/local/lib -L/usr/lib -Wl,-rpath,/usr/lib -o filterBam filterBam.o initOptions.o printElapsedTime.o MatePairs.o PairednessCoverage.o BamToolsAccess.o -lbamtools -lz mkdir -p ../../../bin mv filterBam ../../../bin/filterBam make[3]: Leaving directory '/wrkdirs/usr/ports/biology/augustus/work/Augustus-3.5.0/auxprogs/filterBam/src' make[2]: Leaving directory '/wrkdirs/usr/ports/biology/augustus/work/Augustus-3.5.0/auxprogs/filterBam' cd homGeneMapping; make; make[2]: Entering directory '/wrkdirs/usr/ports/biology/augustus/work/Augustus-3.5.0/auxprogs/homGeneMapping' (cd src; make) make[3]: Entering directory '/wrkdirs/usr/ports/biology/augustus/work/Augustus-3.5.0/auxprogs/homGeneMapping/src' 1 warning generated. c++ -isystem /usr/local/include -DBOOST -DM_SQLITE -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -O2 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I../include -c gene.cc c++ -isystem /usr/local/include -DBOOST -DM_SQLITE -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -O2 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I../include -c genome.cc c++ -isystem /usr/local/include -DBOOST -DM_SQLITE -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -O2 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -I../include -c sqliteDB.cc 1 warning generated. cp -f load2db ../bin/ cp -f fastBlockSearch ../bin/ cp -f pp_simScore ../bin/ In file included from genomicMSA.cc:10: In file included from ../include/genomicMSA.hh:11: ../include/alignment.hh:238:89: warning: binding reference member 'a' to stack allocated parameter 'a_' [-Wdangling-field] 238 | IdxSortCriterion(vector const a_, size_t speciesIdx) : s(speciesIdx), a(a_) {}; | ^~ ../include/alignment.hh:253:31: note: reference member declared here 253 | vector const &a; | ^ 1 warning generated. In file included from geneMSA.cc:11: In file included from ../include/genomicMSA.hh:11: ../include/alignment.hh:238:89: warning: binding reference member 'a' to stack allocated parameter 'a_' [-Wdangling-field] 238 | IdxSortCriterion(vector const a_, size_t speciesIdx) : s(speciesIdx), a(a_) {}; | ^~ ../include/alignment.hh:253:31: note: reference member declared here 253 | vector const &a; | ^ 1 warning generated. In file included from compgenepred.cc:8: In file included from ../include/compgenepred.hh:15: In file included from ../include/geneMSA.hh:12: ../include/alignment.hh:238:89: warning: binding reference member 'a' to stack allocated parameter 'a_' [-Wdangling-field] 238 | IdxSortCriterion(vector const a_, size_t speciesIdx) : s(speciesIdx), a(a_) {}; | ^~ ../include/alignment.hh:253:31: note: reference member declared here 253 | vector const &a; | ^ 1 warning generated. c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -L/usr/local/lib/mysql -L/usr/local/lib -I../include -I/usr/include/lpsolve -I/usr/include/mysql -o augustus augustus.cc genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o types.o gene.o evaluation.o motif.o geneticcode.o hints.o extrinsicinfo.o projectio.o intronmodel.o exonmodel.o igenicmodel.o utrmodel.o merkmal.o vitmatrix.o lldouble.o mea.o graph.o meaPath.o exoncand.o randseqaccess.o fasta.o ncmodel.o parser/parse.o scanner/lex.o genomicMSA.o geneMSA.o contTimeMC.o codonevo.o compgenepred.o phylotree.o orthograph.o orthoexon.o alignment.o speciesgraph.o codonMSA.o train_logReg_param.o tokenizer.o sqliteDB.o dummy.o -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lboost_serialization -lmysqlclient -lmysqlpp -lsqlite3 c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -L/usr/local/lib/mysql -L/usr/local/lib -I../include -I/usr/include/lpsolve -I/usr/include/mysql -o etraining etraining.cc commontrain.o igenictrain.o introntrain.o exontrain.o utrtrain.o genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o types.o gene.o evaluation.o motif.o geneticcode.o hints.o extrinsicinfo.o projectio.o intronmodel.o exonmodel.o igenicmodel.o utrmodel.o merkmal.o vitmatrix.o lldouble.o mea.o graph.o meaPath.o exoncand.o randseqaccess.o fasta.o ncmodel.o parser/parse.o scanner/lex.o genomicMSA.o geneMSA.o contTimeMC.o codonevo.o compgenepred.o phylotree.o orthograph.o orthoexon.o alignment.o speciesgraph.o codonMSA.o train_logReg_param.o tokenizer.o sqliteDB.o -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lboost_serialization -lmysqlclient -lmysqlpp -lsqlite3 c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -L/usr/local/lib/mysql -L/usr/local/lib -I../include -I/usr/include/lpsolve -I/usr/include/mysql -o getSeq getSeq.cc genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o types.o gene.o evaluation.o motif.o geneticcode.o hints.o extrinsicinfo.o projectio.o intronmodel.o exonmodel.o igenicmodel.o utrmodel.o merkmal.o vitmatrix.o lldouble.o mea.o graph.o meaPath.o exoncand.o randseqaccess.o fasta.o ncmodel.o parser/parse.o scanner/lex.o genomicMSA.o geneMSA.o contTimeMC.o codonevo.o compgenepred.o phylotree.o orthograph.o orthoexon.o alignment.o speciesgraph.o codonMSA.o train_logReg_param.o tokenizer.o sqliteDB.o dummy.o -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lboost_serialization -lmysqlclient -lmysqlpp -lsqlite3 In file included from augustus.cc:21: In file included from ../include/compgenepred.hh:15: In file included from ../include/geneMSA.hh:12: ../include/alignment.hh:238:89: warning: binding reference member 'a' to stack allocated parameter 'a_' [-Wdangling-field] 238 | IdxSortCriterion(vector const a_, size_t speciesIdx) : s(speciesIdx), a(a_) {}; | ^~ ../include/alignment.hh:253:31: note: reference member declared here 253 | vector const &a; | ^ c++ -isystem /usr/local/include -DBOOST -DM_SQLITE -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -O2 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -L/usr/local/lib/mysql -L/usr/local/lib -I../include -o homGeneMapping main.cc gene.o genome.o sqliteDB.o -lsqlite3 cp -f getSeq ../bin/ cp -f etraining ../bin/ 1 warning generated. cp -f augustus ../bin/ gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/augustus/work/Augustus-3.5.0/src' mkdir -p ../../../bin/ cp -f homGeneMapping ../../../bin/homGeneMapping make[3]: Leaving directory '/wrkdirs/usr/ports/biology/augustus/work/Augustus-3.5.0/auxprogs/homGeneMapping/src' make[2]: Leaving directory '/wrkdirs/usr/ports/biology/augustus/work/Augustus-3.5.0/auxprogs/homGeneMapping' cd joingenes; make; make[2]: Entering directory '/wrkdirs/usr/ports/biology/augustus/work/Augustus-3.5.0/auxprogs/joingenes' c++ -isystem /usr/local/include -Wall -std=gnu++0x -O2 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -c joingenes.cpp c++ -isystem /usr/local/include -Wall -std=gnu++0x -O2 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -c jg_transcript.cpp c++ -isystem /usr/local/include -Wall -std=gnu++0x -O2 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -c jg_ios.cpp c++ -isystem /usr/local/include -Wall -std=gnu++0x -O2 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -L/usr/local/lib/mysql -L/usr/local/lib -o joingenes joingenes.o jg_transcript.o jg_ios.o mkdir -p ../../bin/ cp -f joingenes ../../bin/ make[2]: Leaving directory '/wrkdirs/usr/ports/biology/augustus/work/Augustus-3.5.0/auxprogs/joingenes' cd utrrnaseq; make; make[2]: Entering directory '/wrkdirs/usr/ports/biology/augustus/work/Augustus-3.5.0/auxprogs/utrrnaseq' mkdir -p build Building file: src/Compute_UTRs.cpp Building file: src/Coord_Transform.cpp Invoking: GCC C++ Compiler: c++ c++ -isystem /usr/local/include -Wall -O0 -pedantic -fmessage-length=0 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -c -MMD -MP -MF"build/Coord_Transform.d" -MT"build/Coord_Transform.o" -o "build/Coord_Transform.o" "src/Coord_Transform.cpp" Invoking: GCC C++ Compiler: c++ c++ -isystem /usr/local/include -Wall -O0 -pedantic -fmessage-length=0 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -c -MMD -MP -MF"build/Compute_UTRs.d" -MT"build/Compute_UTRs.o" -o "build/Compute_UTRs.o" "src/Compute_UTRs.cpp" Building file: src/Genomic_Data.cpp Building file: src/Splice_Sites.cpp Invoking: GCC C++ Compiler: c++ c++ -isystem /usr/local/include -Wall -O0 -pedantic -fmessage-length=0 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -c -MMD -MP -MF"build/Genomic_Data.d" -MT"build/Genomic_Data.o" -o "build/Genomic_Data.o" "src/Genomic_Data.cpp" Invoking: GCC C++ Compiler: c++ c++ -isystem /usr/local/include -Wall -O0 -pedantic -fmessage-length=0 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -c -MMD -MP -MF"build/Splice_Sites.d" -MT"build/Splice_Sites.o" -o "build/Splice_Sites.o" "src/Splice_Sites.cpp" Building file: src/Supporting_Methods.cpp Invoking: GCC C++ Compiler: c++ c++ -isystem /usr/local/include -Wall -O0 -pedantic -fmessage-length=0 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -c -MMD -MP -MF"build/Supporting_Methods.d" -MT"build/Supporting_Methods.o" -o "build/Supporting_Methods.o" "src/Supporting_Methods.cpp" Building file: src/Test.cpp Building file: src/UTRs.cpp Invoking: GCC C++ Compiler: c++ c++ -isystem /usr/local/include -Wall -O0 -pedantic -fmessage-length=0 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -c -MMD -MP -MF"build/UTRs.d" -MT"build/UTRs.o" -o "build/UTRs.o" "src/UTRs.cpp" Invoking: GCC C++ Compiler: c++ c++ -isystem /usr/local/include -Wall -O0 -pedantic -fmessage-length=0 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -c -MMD -MP -MF"build/Test.d" -MT"build/Test.o" -o "build/Test.o" "src/Test.cpp" Building file: src/main.cpp Invoking: GCC C++ Compiler: c++ c++ -isystem /usr/local/include -Wall -O0 -pedantic -fmessage-length=0 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -c -MMD -MP -MF"build/main.d" -MT"build/main.o" -o "build/main.o" "src/main.cpp" src/Coord_Transform.cpp:25:59: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 25 | template struct finding_intron_greater_s : binary_function { | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ src/Coord_Transform.cpp:33:58: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 33 | template struct finding_intron_lesser_s : binary_function { | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ src/Coord_Transform.cpp:41:59: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 41 | template struct finding_intron_greater_e : binary_function { | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ src/Coord_Transform.cpp:49:58: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 49 | template struct finding_intron_lesser_e : binary_function { | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ src/Coord_Transform.cpp:77:7: warning: 'bind2nd, int>' is deprecated [-Wdeprecated-declarations] 77 | bind2nd(finding_intron_greater_s(), i)); | ^ /usr/include/c++/v1/__functional/binder2nd.h:45:1: note: 'bind2nd, int>' has been explicitly marked deprecated here 45 | _LIBCPP_DEPRECATED_IN_CXX11 inline _LIBCPP_HIDE_FROM_ABI binder2nd<_Operation> | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ src/Coord_Transform.cpp:81:7: warning: 'bind2nd, int>' is deprecated [-Wdeprecated-declarations] 81 | bind2nd(finding_intron_greater_e(), i)); | ^ /usr/include/c++/v1/__functional/binder2nd.h:45:1: note: 'bind2nd, int>' has been explicitly marked deprecated here 45 | _LIBCPP_DEPRECATED_IN_CXX11 inline _LIBCPP_HIDE_FROM_ABI binder2nd<_Operation> | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ src/Coord_Transform.cpp:89:7: warning: 'bind2nd, int>' is deprecated [-Wdeprecated-declarations] 89 | bind2nd(finding_intron_lesser_e(), i)); | ^ /usr/include/c++/v1/__functional/binder2nd.h:45:1: note: 'bind2nd, int>' has been explicitly marked deprecated here 45 | _LIBCPP_DEPRECATED_IN_CXX11 inline _LIBCPP_HIDE_FROM_ABI binder2nd<_Operation> | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ src/Coord_Transform.cpp:93:7: warning: 'bind2nd, int>' is deprecated [-Wdeprecated-declarations] 93 | bind2nd(finding_intron_lesser_s(), i)); | ^ /usr/include/c++/v1/__functional/binder2nd.h:45:1: note: 'bind2nd, int>' has been explicitly marked deprecated here 45 | _LIBCPP_DEPRECATED_IN_CXX11 inline _LIBCPP_HIDE_FROM_ABI binder2nd<_Operation> | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 8 warnings generated. Finished building: src/Coord_Transform.cpp Finished building: src/Compute_UTRs.cpp Finished building: src/Supporting_Methods.cpp Finished building: src/Test.cpp src/Splice_Sites.cpp:108:14: warning: result of comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare] 108 | if (all_pos != raw_sp_sites.npos) { //"all" found | ~~~~~~~ ^ ~~~~~~~~~~~~~~~~~ 1 warning generated. Finished building: src/Splice_Sites.cpp Finished building: src/main.cpp Finished building: src/Genomic_Data.cpp src/UTRs.cpp:83:2: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 83 | binary_function { | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ src/UTRs.cpp:92:2: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 92 | binary_function { | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ src/UTRs.cpp:100:59: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 100 | template struct finding_intron_greater_s : binary_function { | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ src/UTRs.cpp:108:58: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 108 | template struct finding_intron_lesser_s : binary_function { | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ src/UTRs.cpp:116:59: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 116 | template struct finding_intron_greater_e : binary_function { | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ src/UTRs.cpp:124:58: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 124 | template struct finding_intron_lesser_e : binary_function { | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ src/UTRs.cpp:133:49: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 133 | template struct finding_repeat : binary_function { | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ src/UTRs.cpp:181:8: warning: 'bind2nd, unsigned int>' is deprecated [-Wdeprecated-declarations] 181 | bind2nd(finding_coding_region_greater(), pos)) : | ^ /usr/include/c++/v1/__functional/binder2nd.h:45:1: note: 'bind2nd, unsigned int>' has been explicitly marked deprecated here 45 | _LIBCPP_DEPRECATED_IN_CXX11 inline _LIBCPP_HIDE_FROM_ABI binder2nd<_Operation> | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ src/UTRs.cpp:183:9: warning: 'bind2nd, unsigned int>' is deprecated [-Wdeprecated-declarations] 183 | bind2nd(finding_coding_region_lesser(), pos)); | ^ /usr/include/c++/v1/__functional/binder2nd.h:45:1: note: 'bind2nd, unsigned int>' has been explicitly marked deprecated here 45 | _LIBCPP_DEPRECATED_IN_CXX11 inline _LIBCPP_HIDE_FROM_ABI binder2nd<_Operation> | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ src/UTRs.cpp:196:49: warning: 'bind2nd, unsigned int>' is deprecated [-Wdeprecated-declarations] 196 | it = find_if(repeats->begin(), repeats->end(), bind2nd(finding_repeat(), start)); | ^ /usr/include/c++/v1/__functional/binder2nd.h:45:1: note: 'bind2nd, unsigned int>' has been explicitly marked deprecated here 45 | _LIBCPP_DEPRECATED_IN_CXX11 inline _LIBCPP_HIDE_FROM_ABI binder2nd<_Operation> | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ src/UTRs.cpp:233:51: warning: 'bind2nd, unsigned int>' is deprecated [-Wdeprecated-declarations] 233 | it = find_if(introns->begin(), introns->end(), bind2nd(finding_intron_greater_s(), start)); | ^ /usr/include/c++/v1/__functional/binder2nd.h:45:1: note: 'bind2nd, unsigned int>' has been explicitly marked deprecated here 45 | _LIBCPP_DEPRECATED_IN_CXX11 inline _LIBCPP_HIDE_FROM_ABI binder2nd<_Operation> | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ src/UTRs.cpp:240:51: warning: 'bind2nd, unsigned int>' is deprecated [-Wdeprecated-declarations] 240 | it = find_if(introns->begin(), introns->end(), bind2nd(finding_intron_greater_e(), start)); | ^ /usr/include/c++/v1/__functional/binder2nd.h:45:1: note: 'bind2nd, unsigned int>' has been explicitly marked deprecated here 45 | _LIBCPP_DEPRECATED_IN_CXX11 inline _LIBCPP_HIDE_FROM_ABI binder2nd<_Operation> | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ src/UTRs.cpp:252:65: warning: 'bind2nd, unsigned int>' is deprecated [-Wdeprecated-declarations] 252 | it = find_if(reverse_introns.begin(), reverse_introns.end(), bind2nd(finding_intron_lesser_e(), start)); | ^ /usr/include/c++/v1/__functional/binder2nd.h:45:1: note: 'bind2nd, unsigned int>' has been explicitly marked deprecated here 45 | _LIBCPP_DEPRECATED_IN_CXX11 inline _LIBCPP_HIDE_FROM_ABI binder2nd<_Operation> | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ src/UTRs.cpp:259:65: warning: 'bind2nd, unsigned int>' is deprecated [-Wdeprecated-declarations] 259 | it = find_if(reverse_introns.begin(), reverse_introns.end(), bind2nd(finding_intron_lesser_s(), start)); | ^ /usr/include/c++/v1/__functional/binder2nd.h:45:1: note: 'bind2nd, unsigned int>' has been explicitly marked deprecated here 45 | _LIBCPP_DEPRECATED_IN_CXX11 inline _LIBCPP_HIDE_FROM_ABI binder2nd<_Operation> | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 14 warnings generated. Finished building: src/UTRs.cpp Building target: utrrnaseq Invoking: GCC C++ Linker c++ -isystem /usr/local/include -Wall -O0 -pedantic -fmessage-length=0 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -std=c++14 -L/usr/local/lib/mysql -L/usr/local/lib -o utrrnaseq build/Compute_UTRs.o build/Coord_Transform.o build/Genomic_Data.o build/Splice_Sites.o build/Supporting_Methods.o build/Test.o build/UTRs.o build/main.o Finished building target: utrrnaseq make[2]: Leaving directory '/wrkdirs/usr/ports/biology/augustus/work/Augustus-3.5.0/auxprogs/utrrnaseq' cd bam2wig; make; make[2]: Entering directory '/wrkdirs/usr/ports/biology/augustus/work/Augustus-3.5.0/auxprogs/bam2wig' cc -isystem /usr/local/include -Wall -O2 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/include/htslib -I/usr/local/include/htslib/ -c bam2wig.c cc -isystem /usr/local/include -Wall -O2 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -L/usr/local/lib/mysql -L/usr/local/lib -o bam2wig bam2wig.o -lhts -lz -lpthread mkdir -p ../../bin cp -f bam2wig ../../bin/bam2wig make[2]: Leaving directory '/wrkdirs/usr/ports/biology/augustus/work/Augustus-3.5.0/auxprogs/bam2wig' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/augustus/work/Augustus-3.5.0/auxprogs' =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> augustus-gene-prediction-3.5.0_17 depends on executable: samtools - not found ===> Installing existing package /packages/All/samtools-1.22.pkg [pkg.DaveG.ca] Installing samtools-1.22... [pkg.DaveG.ca] Extracting samtools-1.22: .......... done ===> augustus-gene-prediction-3.5.0_17 depends on executable: samtools - found ===> Returning to build of augustus-gene-prediction-3.5.0_17 ===> augustus-gene-prediction-3.5.0_17 depends on file: /usr/local/bin/python3.11 - found ===> augustus-gene-prediction-3.5.0_17 depends on package: perl5>=5.42.r<5.43 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for augustus-gene-prediction-3.5.0_17 ===> Generating temporary packing list if [ ! /wrkdirs/usr/ports/biology/augustus/work/Augustus-3.5.0 -ef /wrkdirs/usr/ports/biology/augustus/work/stage/usr/local/augustus ] ; then \ install -d /wrkdirs/usr/ports/biology/augustus/work/stage/usr/local/augustus && \ cp -a config bin scripts /wrkdirs/usr/ports/biology/augustus/work/stage/usr/local/augustus ; \ fi install -l rs /wrkdirs/usr/ports/biology/augustus/work/stage/usr/local/augustus/bin/augustus /wrkdirs/usr/ports/biology/augustus/work/stage/usr/local/bin/augustus install -l rs /wrkdirs/usr/ports/biology/augustus/work/stage/usr/local/augustus/bin/etraining /wrkdirs/usr/ports/biology/augustus/work/stage/usr/local/bin/etraining install -l rs /wrkdirs/usr/ports/biology/augustus/work/stage/usr/local/augustus/bin/prepareAlign /wrkdirs/usr/ports/biology/augustus/work/stage/usr/local/bin/prepareAlign install -l rs /wrkdirs/usr/ports/biology/augustus/work/stage/usr/local/augustus/bin/fastBlockSearch /wrkdirs/usr/ports/biology/augustus/work/stage/usr/local/bin/fastBlockSearch if [ -f /wrkdirs/usr/ports/biology/augustus/work/stage/usr/local/augustus/bin/load2db ] ; then install -l rs /wrkdirs/usr/ports/biology/augustus/work/stage/usr/local/augustus/bin/load2db /wrkdirs/usr/ports/biology/augustus/work/stage/usr/local/bin/load2db ; fi if [ -f /wrkdirs/usr/ports/biology/augustus/work/stage/usr/local/augustus/bin/getSeq ] ; then install -l rs /wrkdirs/usr/ports/biology/augustus/work/stage/usr/local/augustus/bin/getSeq /wrkdirs/usr/ports/biology/augustus/work/stage/usr/local/bin/getSeq ; fi ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2026-03-13T05:00:40+0000' 'PKG_NOTE_ports_top_git_hash=26b198eb3ee3' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=2e4f3d1acf81' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.2' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for augustus-gene-prediction-3.5.0_17 ===> Building augustus-gene-prediction-3.5.0_17 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for augustus-gene-prediction-3.5.0_17 build of biology/augustus | augustus-gene-prediction-3.5.0_17 ended at Fri Mar 13 01:03:58 EDT 2026 build time: 00:03:18