=>> Building biology/augustus build started at Tue May 6 10:33:41 BST 2025 port directory: /usr/ports/biology/augustus package name: augustus-gene-prediction-3.5.0_13 building for: FreeBSD pkg-builder.dan.net.uk 14.2-RELEASE FreeBSD 14.2-RELEASE amd64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1209 Feb 16 09:27 /usr/ports/biology/augustus/Makefile Ports top last git commit: 5529c5919b Ports top unclean checkout: yes Port dir last git commit: fa53920e72 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1402000 Jail OSVERSION: 1402000 Job Id: 04 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1402000 UNAME_v=FreeBSD 14.2-RELEASE UNAME_r=14.2-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/14-amd64-default-dan/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=screen OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/14-amd64-default-dan/04/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=14-amd64-default-dan SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/14-amd64-default-dan/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 -fstack-protector-strong -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_EXT_SUFFIX=.cpython-311 PYTHON_VER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" OSREL=14.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.36.3 PERL_VER=5.36 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/5.36 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_EXT_SUFFIX=.cpython-311 PYTHON_VER=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--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### CCACHE_CPP2=1 WITH_SSP_PORTS=yes WITH_SSP=yes #WITH_LTO=yes DISABLE_LICENSES=yes LICENSES_ACCEPTED=AGPLv3 APACHE10 APACHE11 APACHE20 ART10 ARTPERL10 ART20 BSD BSD2CLAUSE BSD3CLAUSE BSD4CLAUSE BSL CC0-1.0 CDDL ClArtistic EPL GFDL GMGPL GPLv1 GPLv2 GPLv3 GPLv3RLE ISCL LGPL20 LGPL21 LGPL3 LPPL10 LPPL11 LPPL12 LPPL13 LPPL13a LPPL13b LPPL13c MIT MPL OpenSSL OFL10 OFL11 OWL PostgreSQL PHP202 PHP30 PHP301 PSFL RUBY ZLIB ZPL21 SVM-Light EULA ALASIR Microsoft-exFAT SIMIAN UDEVGAME unknown MTA COMMERCIAL teamspeak NO_LICENSES_DIALOGS=yes #### #### NO_IGNORE=yes DEFAULT_VERSIONS+=ssl=openssl apache=2.4 imagemagick=7 java=21 linux=c7 mysql=8.0 php=8.3 samba=4.19 varnish=7 WITH_SETID_MODE=force PHP_ZTS=enabled OPTIONS_UNSET+=OPENJPEG OPTIONS_UNSET+=GSSAPI_BASE OPTIONS_SET+=ZTS OPTIONS_SET+=GSSAPI_NONE ALLOW_UNSUPPORTED_SYSTEM=yes WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited 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_13 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.1.2.pkg [pkg-builder.dan.net.uk] Installing pkg-2.1.2... [pkg-builder.dan.net.uk] Extracting pkg-2.1.2: .......... done ===> augustus-gene-prediction-3.5.0_13 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of augustus-gene-prediction-3.5.0_13 =========================================================================== =================================================== ===== 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_13 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by augustus-gene-prediction-3.5.0_13 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_13 for building ===> Extracting for augustus-gene-prediction-3.5.0_13 => 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_13 ===> Applying FreeBSD patches for augustus-gene-prediction-3.5.0_13 from /usr/ports/biology/augustus/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> augustus-gene-prediction-3.5.0_13 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [pkg-builder.dan.net.uk] Installing gmake-4.4.1... [pkg-builder.dan.net.uk] `-- Installing gettext-runtime-0.23.1... [pkg-builder.dan.net.uk] | `-- Installing indexinfo-0.3.1_1... [pkg-builder.dan.net.uk] | `-- Extracting indexinfo-0.3.1_1: . done [pkg-builder.dan.net.uk] `-- Extracting gettext-runtime-0.23.1: .......... done [pkg-builder.dan.net.uk] Extracting gmake-4.4.1: .......... done ===> augustus-gene-prediction-3.5.0_13 depends on package: gmake>=4.4.1 - found ===> Returning to build of augustus-gene-prediction-3.5.0_13 ===> augustus-gene-prediction-3.5.0_13 depends on file: /usr/local/bin/python3.11 - not found ===> Installing existing package /packages/All/python311-3.11.12.pkg [pkg-builder.dan.net.uk] Installing python311-3.11.12... [pkg-builder.dan.net.uk] `-- Installing libffi-3.4.8... [pkg-builder.dan.net.uk] `-- Extracting libffi-3.4.8: .......... done [pkg-builder.dan.net.uk] `-- Installing mpdecimal-4.0.0... [pkg-builder.dan.net.uk] `-- Extracting mpdecimal-4.0.0: .......... done [pkg-builder.dan.net.uk] `-- Installing openssl-3.0.16,1... [pkg-builder.dan.net.uk] `-- Extracting openssl-3.0.16,1: .......... done [pkg-builder.dan.net.uk] `-- Installing readline-8.2.13_2... [pkg-builder.dan.net.uk] `-- Extracting readline-8.2.13_2: .......... done [pkg-builder.dan.net.uk] Extracting python311-3.11.12: .......... done ===== Message from python311-3.11.12: -- 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_13 depends on file: /usr/local/bin/python3.11 - found ===> Returning to build of augustus-gene-prediction-3.5.0_13 ===> augustus-gene-prediction-3.5.0_13 depends on package: perl5>=5.36<5.37 - not found ===> Installing existing package /packages/All/perl5-5.36.3_3.pkg [pkg-builder.dan.net.uk] Installing perl5-5.36.3_3... [pkg-builder.dan.net.uk] Extracting perl5-5.36.3_3: .......... done ===> augustus-gene-prediction-3.5.0_13 depends on package: perl5>=5.36<5.37 - found ===> Returning to build of augustus-gene-prediction-3.5.0_13 ===> augustus-gene-prediction-3.5.0_13 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg-builder.dan.net.uk] Installing ccache-3.7.12_8... [pkg-builder.dan.net.uk] 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_13 depends on file: /usr/local/bin/ccache - found ===> Returning to build of augustus-gene-prediction-3.5.0_13 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> augustus-gene-prediction-3.5.0_13 depends on shared library: libbamtools.so - not found ===> Installing existing package /packages/All/bamtools-2.5.2_2.pkg [pkg-builder.dan.net.uk] Installing bamtools-2.5.2_2... [pkg-builder.dan.net.uk] `-- Installing jsoncpp-1.9.6_1... [pkg-builder.dan.net.uk] `-- Extracting jsoncpp-1.9.6_1: .......... done [pkg-builder.dan.net.uk] Extracting bamtools-2.5.2_2: .......... done ===> augustus-gene-prediction-3.5.0_13 depends on shared library: libbamtools.so - found (/usr/local/lib/libbamtools.so) ===> Returning to build of augustus-gene-prediction-3.5.0_13 ===> augustus-gene-prediction-3.5.0_13 depends on shared library: libboost_iostreams.so - not found ===> Installing existing package /packages/All/boost-libs-1.87.0_1.pkg [pkg-builder.dan.net.uk] Installing boost-libs-1.87.0_1... [pkg-builder.dan.net.uk] `-- Installing icu-76.1,1... [pkg-builder.dan.net.uk] `-- Extracting icu-76.1,1: .......... done [pkg-builder.dan.net.uk] Extracting boost-libs-1.87.0_1: .......... done ===== Message from boost-libs-1.87.0_1: -- 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_13 depends on shared library: libboost_iostreams.so - found (/usr/local/lib/libboost_iostreams.so) ===> Returning to build of augustus-gene-prediction-3.5.0_13 ===> augustus-gene-prediction-3.5.0_13 depends on shared library: libcolamd.so - not found ===> Installing existing package /packages/All/suitesparse-colamd-3.3.4.pkg [pkg-builder.dan.net.uk] Installing suitesparse-colamd-3.3.4... [pkg-builder.dan.net.uk] `-- Installing gcc13-13.3.0_2... [pkg-builder.dan.net.uk] | `-- Installing binutils-2.44,1... [pkg-builder.dan.net.uk] | | `-- Installing zstd-1.5.7... [pkg-builder.dan.net.uk] | | `-- Installing liblz4-1.10.0,1... [pkg-builder.dan.net.uk] | | `-- Extracting liblz4-1.10.0,1: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting zstd-1.5.7: .......... done [pkg-builder.dan.net.uk] | `-- Extracting binutils-2.44,1: .......... done [pkg-builder.dan.net.uk] | `-- Installing gmp-6.3.0... [pkg-builder.dan.net.uk] | `-- Extracting gmp-6.3.0: .......... done [pkg-builder.dan.net.uk] | `-- Installing mpc-1.3.1_1... [pkg-builder.dan.net.uk] | | `-- Installing mpfr-4.2.2,1... [pkg-builder.dan.net.uk] | | `-- Extracting mpfr-4.2.2,1: .......... done [pkg-builder.dan.net.uk] | `-- Extracting mpc-1.3.1_1: ...... done [pkg-builder.dan.net.uk] `-- Extracting gcc13-13.3.0_2: .......... done create symlink for gcc13 create symlink for gcc13 (world) create symlink for g++13 create symlink for g++13 (world) create symlink for cpp13 create symlink for cpp13 (world) [pkg-builder.dan.net.uk] `-- Installing suitesparse-config-7.10.2... [pkg-builder.dan.net.uk] | `-- Installing openblas-0.3.29_1,2... [pkg-builder.dan.net.uk] | `-- Extracting openblas-0.3.29_1,2: .......... done [pkg-builder.dan.net.uk] `-- Extracting suitesparse-config-7.10.2: .......... done [pkg-builder.dan.net.uk] Extracting suitesparse-colamd-3.3.4: .......... done ===== Message from gcc13-13.3.0_2: -- 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/gcc13 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> augustus-gene-prediction-3.5.0_13 depends on shared library: libcolamd.so - found (/usr/local/lib/libcolamd.so) ===> Returning to build of augustus-gene-prediction-3.5.0_13 ===> augustus-gene-prediction-3.5.0_13 depends on shared library: libgsl.so - not found ===> Installing existing package /packages/All/gsl-2.7.1_1.pkg [pkg-builder.dan.net.uk] Installing gsl-2.7.1_1... [pkg-builder.dan.net.uk] Extracting gsl-2.7.1_1: .......... done ===> augustus-gene-prediction-3.5.0_13 depends on shared library: libgsl.so - found (/usr/local/lib/libgsl.so) ===> Returning to build of augustus-gene-prediction-3.5.0_13 ===> augustus-gene-prediction-3.5.0_13 depends on shared library: libhts.so - not found ===> Installing existing package /packages/All/htslib-1.21.pkg [pkg-builder.dan.net.uk] Installing htslib-1.21... [pkg-builder.dan.net.uk] `-- Installing curl-8.13.0_1... [pkg-builder.dan.net.uk] | `-- Installing brotli-1.1.0,1... [pkg-builder.dan.net.uk] | `-- Extracting brotli-1.1.0,1: .......... done [pkg-builder.dan.net.uk] | `-- Installing libidn2-2.3.8... [pkg-builder.dan.net.uk] | | `-- Installing libunistring-1.3... [pkg-builder.dan.net.uk] | | `-- Extracting libunistring-1.3: .......... done [pkg-builder.dan.net.uk] | `-- Extracting libidn2-2.3.8: .......... done [pkg-builder.dan.net.uk] | `-- Installing libnghttp2-1.65.0... [pkg-builder.dan.net.uk] | `-- Extracting libnghttp2-1.65.0: ....... done [pkg-builder.dan.net.uk] | `-- Installing libssh2-1.11.1,3... [pkg-builder.dan.net.uk] | `-- Extracting libssh2-1.11.1,3: .......... done [pkg-builder.dan.net.uk] `-- Extracting curl-8.13.0_1: .......... done [pkg-builder.dan.net.uk] `-- Installing libdeflate-1.22... [pkg-builder.dan.net.uk] `-- Extracting libdeflate-1.22: .......... done [pkg-builder.dan.net.uk] Extracting htslib-1.21: .......... done ===> augustus-gene-prediction-3.5.0_13 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> Returning to build of augustus-gene-prediction-3.5.0_13 ===> augustus-gene-prediction-3.5.0_13 depends on shared library: liblpsolve55.so - not found ===> Installing existing package /packages/All/lp_solve-5.5.2.5_1.pkg [pkg-builder.dan.net.uk] Installing lp_solve-5.5.2.5_1... [pkg-builder.dan.net.uk] Extracting lp_solve-5.5.2.5_1: .......... done ===> augustus-gene-prediction-3.5.0_13 depends on shared library: liblpsolve55.so - found (/usr/local/lib/liblpsolve55.so) ===> Returning to build of augustus-gene-prediction-3.5.0_13 ===> augustus-gene-prediction-3.5.0_13 depends on shared library: libmysqlpp.so - not found ===> Installing existing package /packages/All/mysql++-3.3.0.pkg [pkg-builder.dan.net.uk] Installing mysql++-3.3.0... [pkg-builder.dan.net.uk] `-- Installing mysql80-client-8.0.42... [pkg-builder.dan.net.uk] | `-- Installing cyrus-sasl-2.1.28_5... *** Added group `cyrus' (id 60) *** Added user `cyrus' (id 60) [pkg-builder.dan.net.uk] | `-- Extracting cyrus-sasl-2.1.28_5: .......... done [pkg-builder.dan.net.uk] | `-- Installing groff-1.23.0_4... [pkg-builder.dan.net.uk] | | `-- Installing libiconv-1.17_1... [pkg-builder.dan.net.uk] | | `-- Extracting libiconv-1.17_1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing psutils-1.17_6... [pkg-builder.dan.net.uk] | | `-- Installing libpaper-1.1.28_1... [pkg-builder.dan.net.uk] | | `-- Extracting libpaper-1.1.28_1: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting psutils-1.17_6: .......... done [pkg-builder.dan.net.uk] | | `-- Installing uchardet-0.0.8_1... [pkg-builder.dan.net.uk] | | `-- Extracting uchardet-0.0.8_1: .......... done [pkg-builder.dan.net.uk] | `-- Extracting groff-1.23.0_4: .......... done [pkg-builder.dan.net.uk] | `-- Installing hidapi-0.14.0... [pkg-builder.dan.net.uk] | `-- Extracting hidapi-0.14.0: .......... done [pkg-builder.dan.net.uk] | `-- Installing libedit-3.1.20250104,1... [pkg-builder.dan.net.uk] | `-- Extracting libedit-3.1.20250104,1: .......... done [pkg-builder.dan.net.uk] | `-- Installing libevent-2.1.12... [pkg-builder.dan.net.uk] | `-- Extracting libevent-2.1.12: .......... done [pkg-builder.dan.net.uk] | `-- Installing libfido2-1.15.0... [pkg-builder.dan.net.uk] | | `-- Installing libcbor-0.12.0... [pkg-builder.dan.net.uk] | | `-- Installing libcjson-1.7.18_2... [pkg-builder.dan.net.uk] | | `-- Extracting libcjson-1.7.18_2: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting libcbor-0.12.0: .......... done [pkg-builder.dan.net.uk] | `-- Extracting libfido2-1.15.0: .......... done [pkg-builder.dan.net.uk] | `-- Installing libunwind-20240221_2... [pkg-builder.dan.net.uk] | `-- Extracting libunwind-20240221_2: .......... done [pkg-builder.dan.net.uk] | `-- Installing openldap26-client-2.6.9_1... [pkg-builder.dan.net.uk] | `-- Extracting openldap26-client-2.6.9_1: .......... done [pkg-builder.dan.net.uk] `-- Extracting mysql80-client-8.0.42: .......... done [pkg-builder.dan.net.uk] 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-1.23.0_4: -- In order to be able to use the html driver, you need to install the following packages: - ghostscript - netpbm -- ===> NOTICE: The groff port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing ===== Message from openldap26-client-2.6.9_1: -- 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-8.0.42: -- This is the mysql CLIENT without the server. for complete server and client, please install databases/mysql80-server ===> augustus-gene-prediction-3.5.0_13 depends on shared library: libmysqlpp.so - found (/usr/local/lib/libmysqlpp.so) ===> Returning to build of augustus-gene-prediction-3.5.0_13 ===> augustus-gene-prediction-3.5.0_13 depends on shared library: libmysqlclient.so.21 - found (/usr/local/lib/mysql/libmysqlclient.so.21) ===> augustus-gene-prediction-3.5.0_13 depends on shared library: libsqlite3.so - not found ===> Installing existing package /packages/All/sqlite3-3.46.1_1,1.pkg [pkg-builder.dan.net.uk] Installing sqlite3-3.46.1_1,1... [pkg-builder.dan.net.uk] Extracting sqlite3-3.46.1_1,1: ......... done ===> augustus-gene-prediction-3.5.0_13 depends on shared library: libsqlite3.so - found (/usr/local/lib/libsqlite3.so) ===> Returning to build of augustus-gene-prediction-3.5.0_13 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for augustus-gene-prediction-3.5.0_13 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for augustus-gene-prediction-3.5.0_13 mkdir -p bin cd src && /usr/local/bin/gmake gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/augustus/work/Augustus-3.5.0/src' 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 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 -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 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. 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 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. 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 mea.cc:326:29: warning: variable 'codlength' set but not used [-Wunused-but-set-variable] 326 | int transStart, transEnd, codlength = 0; | ^ 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 -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 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. 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 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. 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 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. 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 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. 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 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 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o phylotree.o phylotree.cc 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. 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 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. 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 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. 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 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:998:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX14' 998 | # define _LIBCPP_DEPRECATED_IN_CXX14 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 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 -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 -fstack-protector-strong -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 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; | ^ 1 warning generated. cp -f augustus ../bin/ 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 -fstack-protector-strong -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 cp -f etraining ../bin/ 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 -fstack-protector-strong -L/usr/local/lib -o prepareAlign pp_prepare_align.cc cp -f prepareAlign ../bin/ 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 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 -fstack-protector-strong -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 cp -f fastBlockSearch ../bin/ 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 -fstack-protector-strong -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 pp_simscore.cc:870:21: warning: unused variable 'count_miss' [-Wunused-variable] 870 | pair count_miss; | ^~~~~~~~~~ 1 warning generated. cp -f pp_simScore ../bin/ 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 -fstack-protector-strong -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 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){ | ~~~~~~ ^ ~~ 1 warning generated. cp -f load2db ../bin/ 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 -fstack-protector-strong -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 cp -f getSeq ../bin/ 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 -fstack-protector-strong -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 cp -f load2sqlitedb ../bin/ 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 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/augustus/work/Augustus-3.5.0/src' mkdir -p bin cd auxprogs && /usr/local/bin/gmake 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 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 -fstack-protector-strong -L/usr/local/lib -o aln2wig aln2wig.o 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 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 -fstack-protector-strong -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 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 -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 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 -fstack-protector-strong -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 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 -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 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 -fstack-protector-strong -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' 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 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 -fstack-protector-strong -L/usr/local/lib -I../include -o homGeneMapping main.cc gene.o genome.o sqliteDB.o -lsqlite3 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 -fstack-protector-strong -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 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" Finished building: 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" 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 8 warnings generated. Finished building: src/Coord_Transform.cpp Building file: 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/Genomic_Data.d" -MT"build/Genomic_Data.o" -o "build/Genomic_Data.o" "src/Genomic_Data.cpp" Finished building: 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/Splice_Sites.d" -MT"build/Splice_Sites.o" -o "build/Splice_Sites.o" "src/Splice_Sites.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 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" Finished building: src/Supporting_Methods.cpp Building file: src/Test.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" Finished building: 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" 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # 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:992:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 992 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:977:49: note: expanded from macro '_LIBCPP_DEPRECATED' 977 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 14 warnings generated. Finished building: src/UTRs.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" Finished building: src/main.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 -fstack-protector-strong -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 -fstack-protector-strong -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_13 depends on executable: samtools - not found ===> Installing existing package /packages/All/samtools-1.21.pkg [pkg-builder.dan.net.uk] Installing samtools-1.21... [pkg-builder.dan.net.uk] Extracting samtools-1.21: .......... done ===> augustus-gene-prediction-3.5.0_13 depends on executable: samtools - found ===> Returning to build of augustus-gene-prediction-3.5.0_13 ===> augustus-gene-prediction-3.5.0_13 depends on file: /usr/local/bin/python3.11 - found ===> augustus-gene-prediction-3.5.0_13 depends on package: perl5>=5.36<5.37 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for augustus-gene-prediction-3.5.0_13 ===> 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=2025-05-06T09:33:41+0000' 'PKG_NOTE_ports_top_git_hash=5529c5919b' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=fa53920e72' '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_13 ===> Building augustus-gene-prediction-3.5.0_13 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for augustus-gene-prediction-3.5.0_13 build of biology/augustus | augustus-gene-prediction-3.5.0_13 ended at Tue May 6 10:46:57 BST 2025 build time: 00:13:16